Manual Transmission Conversion

Gearbox illustration from Autocar Handbook 1935
Gearbox illustration from Autocar Handbook 1935 [Source]

Donor Purchase and Prep Work

After purchasing my IS300 wagon, I daily drove it for about a year while I fixed any lingering issues from previous owners, like worn control-arm bushings and a bad VVTi solenoid. Meanwhile, I continued researching all parts required for a complete trans swap, and I kept my eye out for W55 manual transmissions on Craigslist, eBay, and forums.

I wanted to integrate the parts as OE-like as possible, as far as wire routing, fasteners, etc. Some “complete” kits were for sale on eBay, but I was uneasy about the quality of parts and how hard it might be to find a replacement for certain things, like the clutch pedal or ECU, if any turned out to be bad. Aside from the many small parts and hardware that were missing, most kits also did not include the section of trans tunnel that needs to be grafted on. I decided to purchase a whole manual-transmission donor car to avoid these issues. I could be confident that all the parts were operational, and I could see exactly how the parts were installed originally so as to mimic the config exactly in my car. So the task became finding the cheapest manual donor car with an intact driveline. I looked at some salvage sites, but the ones I visited weren’t upfront about their practices, so I was leery of putting my eggs in that basket. I was able to score one for $3200 a few hours away. It had a bad clutch, which wasn’t a problem for me since I would install a new one during the swap anyway.

To plan the mechanical parts of the swap, I referenced relevant sections of the FSM (factory service manual), and I read a lot of transmission-swap threads on the forum. I used to access the electronic parts catalog and find part numbers when something needed to be replaced. Sometimes the parts catalog’s exploded views showed something the FSM neglected. In other cases, it helped discern whether a certain P/N differed on auto vs. manual cars. I was even able to search by VIN, comparing my two cars exactly.

A significant part of the job is modifying the auto-trans vehicle’s electrical system to properly operate with a manual transmission. The type of vehicle speed sensor in the trans is different, the gauge cluster is different, the ECM is different, the clutch pedal has two switches that need to be integrated, the reverse lights are actuated by a new switch, etc. The good news is that an automatic trans is more I/O and more-complex I/O than a manual trans, so in the process of converting to the simpler system, many wires in the vehicle harness would become unused. I planned to repurpose now-unused parts of the vehicle harness to carry power and signal for the new circuits. This way I could avoid running new wires through the firewall, in the engine bay, etc. since the OE wire routings are hard to access, and any auxilliary routings would look unprofessional.

The forum was invaluable for getting me started on what changes were needed, especially related to how the instrument cluster relays the speed signal to the ECU. I didn’t find much in the way of wire routing though, so I spent hours studying the wiring diagrams in the FSM. Most of my research and planning focused on the needed electrical modifications.

Components required for the conversion:

  • Transmission, clutch-release fork, rear trans mount
  • Shifter assy
  • Flywheel, clutch, new hardware
  • Driveshaft
  • Clutch master cylinder, slave cylinder, hard line
  • Clutch pedal assembly
  • Brake pedal assembly
  • ECU
  • Instrument cluster
  • Traction-control module
  • Snow/Trac switch assy

In-place modifications required:

  • Drill holes in firewall for clutch master-cyl pushrod and mounting studs
  • Cut out the top of the transmission tunnel and transplant the top section of a manual-trans chassis trans tunnel
  • Wire the M/T ECM’s vehicle-speed signal
  • Wire the transmission’s reverse switch
  • Wire the clutch start switch
  • Wire the clutch cruise-control switch
  • Modify misc. other wiring

Other components different between auto and manual cars that I didn’t replace:

  • Differential (auto one has higher ratio – 3.91 vs. 3.74 M/T version. Left it for more torque)
  • Radiator (auto one has trans cooler pipe in bottom end-tank)
  • Steering wheel (my donor car’s steering wheel was not in great shape; besides, working around airbags is sketchy)
  • Sound insulation along underside of manual-car’s trans tunnel (installed over many small weld studs not present on auto-trans car)
  • Accessory drive belt tensioner (manual one has a damper that attaches from tensioner to frame)

Other parts to replace along the way:

  • Fuel-tank overfill check valve w/ gasket (old one cracked, causing evap CELs P0440 and P0442)
  • Engine rear main seal
  • Exhaust gaskets
  • Gear oil
  • Trans tailshaft seal


Donor Trans Removal

My IS300 and the transmission donor

Here are the steps I followed to remove the manual transmission from the donor car:

  1. Disassemble interior
    1. Remove console trim
    2. Remove shift boot
    3. Remove shift lever
    4. Move driver seat all the way back for easier pedal access later (after batt disconnected)
  2. Remove components in engine bay and under car
    1. Put car on jack stands
    2. Disconnect (-) batt terminal
    3. Remove intake
    4. Remove throttle body
    5. Disconnect upper radiator hose, brake-booster line, and anything else that will prevent engine from tilting back.
    6. Remove exhaust
    7. Remove midpipe (had to cut off rusted exhaust bolts to separate cats/exhaust manifold from midpipe)
    8. Car was missing tailpipe, so nothing to remove there.
    9. Remove cats/exhaust manifold
    10. Drain coolant
  3. Disconnect transmission parts and drop transmission
    1. Drop driveshaft (no center-support spacers present)
    2. Drain trans gear oil
    3. Remove clutch slave cylinder and ground strap from transmission
    4. Disconnect vehicle speed sensor and harness
    5. Disconnect reverse-switch connector
    6. Remove starter
    7. Jack up trans
    8. Break bellhousing bolts loose (using various extensions, wobble extensions, and swivel joints. An impact gun helps, too.
    9. Unbolt trans crossmember
    10. Unbolt bellhousing
    11. Remove trans
  4. Remove more parts from interior
    1. Remove clutch and brake pedals.
    2. Remove instrument cluster
    3. Remove clutch master cylinder and line
    4. Remove ECM
  5. Replace tires, drop car, roll out of garage.
  6. Clean parts

Manual transmission removed


After inspecting the removed parts, I took inventory of what needed to be replaced so new parts would be delivered in time for the install.


Auto Trans Removal

Most of these steps were the same as for the donor car.

  1. Disassemble interior
    1. Remove console trim
    2. Disassemble shifter
  2. Engine bay and under car
    1. Disconnect negative batt terminal (again, moving driver seat all the way back first
    2. Put car on jack stands
    3. Remove wheels
    4. Remove intake
    5. Disconnect upper radiator hose, brake-booster line, and anything else that will prevent engine from tilting back.
    6. Put kroil (penetrating oil) on exhaust hardware
    7. Remove all engine under covers
    8. Drain coolant
    9. Remove exhaust
  3. Disconnect auto trans and remove
    1. Drain trans fluid
    2. Remove dipstick tube/filler pipe
    3. Remove shift control rod
    4. Remove driveshaft (this one has center-support spacers)
    5. Disconnect upper raditator hose
    6. Disconnect and remove trans oil cooler pipes
    7. Disconnect trans electrical connectors
    8. O/D clutch speed sensor
    9. Vehicle speed sensor
    10. Park/neutral position switch
    11. Solenoid
    12. Remove trans ground strap
    13. Remove starter
    14. Unbolt torque converter from flex plate (through window on engine side)
    15. Loosen bellhousing bolts
    16. Put jack under trans
    17. Unbolt rear trans crossmember
    18. Jack up front of engine
    19. Unbolt bellhousing
    20. Remove trans (disconnecting any previously-inaccessible harness clips in the process)
    21. Remove flex plate from crankshaft

Automatic transmission removed

Top: auto | Bottom: manual



Trans-tunnel Shift-surround Transplant

The part of the manual transmission tunnel that is different from the auto chassis is P/N 58261-53021. It is a raised section surrounding the shift turret. It also has a larger opening than the automatic-trans chassis does.

The red donor car was originally silver, so the painted surfaces under the car, in the engine bay, and in the interior are all silver. This can make some of the pictures confusing as to which car is pictured.


Side-by-side manual and auto transmission tunnels
Left: manual | Right: auto


Transmission-tunnel add-on piece 58261-53021
Transmission-tunnel add-on piece 58261-53021 [Source]

I took reference measurements on the two trans tunnels to help in locating the transplanted panel. The manual tunnel’s piece had a weld stud that I drilled a hole for in my tunnel to help locate the piece.

Taking a measurement on the manual trans tunnel


I followed these steps to remove the piece from the donor car and graft it into the wagon’s tunnel:

  1. Cut out trans-tunnel section from donor car. I used an angle grinder (plunge cutting), oscillating multitool (best control for small cuts), and recip saw (best speed).
  2. Cut out smaller section of auto trans tunnel, allowing for overlap of new section
    1. Drill small holes from above to mark corners of cut path
    2. Plunge-cut from below with angle grinder to start each of the four segments. Cutting from below made for easier tool positioning and less sparks in car.
Cutting the auto trans tunnel from below
Cutting the auto trans tunnel from below
    1. Finish cuts with recip saw and oscillating multi-tool from above.
Side-by-side manual and auto transmission tunnels after cutting
Left: manual | Right: auto
  1. Shape tunnel opening and piece to be added
    1. Use angle grinder (grinding-wheel attachment) to shape and smooth edges of add-on piece.
    2. Bend down edges of receiving trans tunnel opening to allow add-on to sit flush.
    3. Make small cuts and bend up front edge of tunnel opening to meet raised add-on edge.
    4. Make small cuts and bend down front edge of add-on piece to match tunnel opening.
  2. Apply touch-up paint to all cuts to prevent rust
  3. Drill holes for rivets
    1. Drill pattern in add-on piece first
    2. Mock up add-on piece and drill through rivet holes to make hole pattern in tunnel. As each hole is completed, drop a rivet in to maintain alignment while drilling subsequent holes.
  4. Install trans-tunnel add-on w/ seam sealer and rivets.
    1. Lay seam sealer bead around tunnel opening (I used “Transtar 4167 Ultra Flex”)

Seam sealer on trans tunnel

    1. Place add-on piece on tunnel
    2. Place all rivets in holes before popping any
    3. Install all rivets. The rivet-gun head wouldn’t fit well next to the panel in some places, so I kept getting bent shanks stuck in gun.
    4. I didn’t get much squeeze-out of the seam sealer, so added more from below and spread it into seams with my finger.
Finished tunnel modification
Finished shift-surround transplant


Fuel-tank Overfill Check Valve Replacement

I had two CELs since I bought the car: P0440 and P0442. My research indicated they were due to a cracked fuel-tank overfill check valve (P/N 77390-53010). I would replace the gasket at the same time (P/N 77177-12020). A lot of people just cut a hole in the body under the seats to access this piece, but I didn’t want to do that if I could avoid it, so I decided to remove the fuel tank from below to access the valve.

Unfortunately, to some extent I was flying blind on the fuel-tank removal since it is not described in the FSM, and I haven’t seen any procedures described online. I just found as many FSM and EPC diagrams of the evap system I could and pieced together what connections I had to deal with.

FSM page SF-28 showing fuel tank and peripherals
Fuel tank diagram (FSM page SF-28)

Fuel-tank and evap canister illustrations
Fuel-tank and evap canister illustrations [Source]
I followed these steps to disconnect and remove the fuel tank:

  1. Remove rear seat (FSM p. BO-204).
  2. Disconnect sender and pump electrical connectors under seat
  3. Disconnect fuel feed line from under seat
  4. Disconnect and move parking-brake lines
  5. Disconnect lines at the back of the tank from bottom (this was the hardest part)
    • Fill pipe
    • Two smaller hoses that go to fill pipe assy
    • One big and one small hose that go to CC assy
  6. Unbolt two steel tank-retention straps and two side support beams (called “Fuel Tank Bands” and “Fuel Tank Protectors” in FSM).
  7. Lower tank slowly, manipulating loose hoses and things to clear the frame.
Fuel tank removed, showing hose connections
Each hose that must be disconnected in step 5 above

I should have thought ahead and run my fuel load down before starting the job. The tank was 3/4 full, making removal more of a challenge. Also, I should have set up a broader base of support under the tank. I just had my jack under the middle, and the sides of the tank (where most of the fuel weight is) started sagging as I released the supports.

I replaced the fuel-tank overfill check valve and gasket. Sure enough, the old valve housing was cracked.

Cracked fuel-tank overfill check valve


Pedal Assy Transplant

Next, it was time to install the clutch pedal assembly from the donor car. The brake pedal assembly also has to be replaced at the same time, since the manual-version “pedal pad” at the bottom is narrower, and the arm it’s welded to is shaped differently as well.


I removed the pedal assys from the donor car, along with the clutch master and slave cylinders and the hydraulic hard lines.

Then I followed these steps to install the parts in my car:

  1. Remove auto brake pedal and misc ECUs/modules (Toyota seems to call every controller an ECU)
  2. Drill stud holes for clutch pedal after taking hole-location measurements on donor car
  3. Drill center-bore hole for CMC pushrod w/ hole saw
The firewall's insulation cutout for clutch MC
The A/T chassis insulation had a punchout for the clutch MC.
Clutch MC holes drilled
New clutch MC holes drilled (viewed from engine bay)
  1. Install pedals and clutch master cylinder – 9 ft-lb (FSM p. CL-5)
New pedals installed
New pedals installed

One thing I noticed was that the manual chassis has a reinforcing plate tack-welded to the firewall to better support clutch-pedal forces. I watched the deflection of the sheet metal while actuating the clutch, and everything is pretty solid, so I didn’t bother to add any reinforcement. (If using a stiffer clutch than my OE-replacement, this could be a problem.)


Wiring Modifications

ECM Speed Signal


  • A/T and M/T ECMs and instrument clusters read vehicle speed differently.
  • A/T speed signal propagation:
    • ABS sensors -> skid-ctrl ECU -> cluster (pin A12) -> A/T ECM (via MPX pins)
    • ECM pin B11 unoccupied
  • M/T speed signal propagation:
    • M/T VSS -> cluster (B1, A12) -> M/T ECM (pin B11)
    • M/T ECM needs speed-signal input at B11, which it doesn’t get in A/T car.
  • Since I’m still using the A/T differential gear, VSS reading will be inaccurate. Want to retain ABS input for speed (both cluster and ECM).
  • Need to splice into speed-signal output from inst cluster A13 and route that to M/T ECM pin B11.

Summary of Modifications:

  • Wired inst cluster A13 (conn C9) to ECM B11 (conn E4).
  • Disconnected grey/red shift-down wire at J/B conn IA1 pos 16 and ECM E4 B5 to repurpose.
    • Re-pinned grey/red shift-down wire from E4 B5 on ECM conn to E4 B11
    • Cut shift-down wire at female J/B conn IA1 pos. 16. Insulated end of grey/red wire that runs up to steering wheel.
    • Spliced new black wire onto IA1 pos. 16 wire and routed to instrument cluster, splicing into existing speed-output wire (not cut) at inst cluster C9 A13 connector.

Since the A/T and M/T cars deliver a speed signal to the ECM in different ways, I had to modify my vehicle harness to ensure the speedometer and ECM still worked properly.

FSM description of ECM speed inputs
FSM description of ECM speed inputs

Many people performing this trans swap will wire the manual-trans VSS (vehicle speed sensor) to the instrument cluster just like M/T OE. However, I had decided to keep the shorter-geared A/T rear diff in my car, so if I wired my trans VSS to the ECM, the speed would be incorrect. So I kept the ABS wheel-speed signal coming into the cluster, leaving the vehicle speed sensor disconnected. The only modification I made to the vehicle harness was to provide the speed signal from cluster to ECM pin B11, where the M/T ECM expected to see speed. I left the multiplexed signals alone, since they carry additional signals.

Diagram of ECM speed signal path for standard A/T or M/T car, along with hybrid approach
Speed signal paths: standard A/T and M/T setup vs. my hybrid approach

I didn’t want to route a new wire through the firewall and the engine bay and into the ECM housing if I could avoid it. I found that one of the wires previously used by the steering-wheel shift buttons would work. I cut this wire in the driver-side junction box and at the ECM, creating a floating segment I could reuse. I connected this to ECM pin B11 at one end and spliced into the instrument-cluster A13 pin.

ECM speed signal modification (harness markup)
Repurposing the steering-wheel electronic shift wire to carry the new speed signal from cluster to ECM

Repurposing an electronic shift-control wire at the ECM connector

Driver-side junction box connector IA1
Driver-side junction box connector IA1

The ECM connectors are challenging to re-pin. Searching online with the connector P/N (found on ToyoDIY) led me to a Toyota Wire Harness Repair Manual that helped significantly (here and with other connectors).

ECM connector illustration
ECM connector de-pinning illustration [source]
What ended up working best for ECM-connector de-pinning was a small needle.

De-pinning an ECM connector


Reverse Switch


  • Need to wire reverse switch from M/T to enable reverse lights and tell ECM when car is in reverse.
  • Existing P1 connector (from A/T) has reverse wires to use.

Summary of Modifications:

  • Removed leads and M/T connector B9 from M/T donor car
  • De-pinned A/T conn P1 pos. 2 and 3, connected them to new wires going to M/T conn B9 pos. 1 and 2, respectively.
  • Conn P1 tied up in engine comp next to horn.

The M/T and A/T harnesses have different connectors for their reverse switches in the transmission, but they signal the ECM the same way – by sending high signal to ECM pin D5 when in reverse. So all I did was de-pin the power supply to the A/T shift-position connector and the wire it uses to relay power to the ECM, and I connected these to the M/T reverse-switch connnector.

Reverse-switch signal modification (harness markup)
Wiring in the new M/T reverse switch in place of the A/T signal
Modifications to the manual-trans harness
Modifications to the manual-trans harness
New reverse wires at A/T connector P1
New reverse wires at A/T connector P1


Clutch Start Switch / Neutral Safety Switch


  • M/T ECM uses a different type of neutral-safety signal than A/T car:
    • A/T-selector (P1 conn) wires send signal when vehicle in Park
    • M/T car sends signal from clutch-down switch
    • Both connect to ECM pin A12
    • Both are in series with ignition switch and must be closed for starter relay coil to energize.
  • Could wire clutch switch in by connecting to wires at unused A/T conn P1, but it’s on other side of firewall.
  • Both the A/T and M/T vehicle harnesses get power from D/S J/B and relay it through P/S J/B J19 before going to starter relay and ECM. So I could tap into the wires inside the cabin at junction boxes.

Summary of Modifications:

  • Removed clutch switch connector and wires from M/T car.
  • Connected existing pin on clutch-switch connector lead to conn 1K pos 8 in place of A/T wire.
  • Extended other wire from clutch-switch connector to get to P/S J/B. After soldering on a short lead (w/ needed terminal) taken from donor car J/B connection, plugged the extended wire into available J19 C cavity. This connects it to the line for energizing the starter relay and signaling ECM E3 A12.
  • Later, added additional theft-deterrent start switch in series with this circuit. Used TRAC OFF switch from A/T car and mating connector H16 removed from M/T car (original TRAC OFF conn T7 broke). Wired into circuit between clutch switch and J19 to act as auxilliary momentary switch that must be held while depressing clutch and turning ignition key.
FSM pages BE-83 and CL-3 showing A/T neutral start switch and M/T clutch start switch
from FSM pages BE-83 and CL-3
Clutch-start switch (harness markup)
Wiring in the new M/T clutch-start switch in place of the A/T shifter signal

Clutch start switch wiring

Auxilliary start switch


Clutch Cruise Switch


  • M/T ECM uses a different type of cruise control-enable signal than M/T car:
    • A/T car uses park/neutral switch position to enable cruise.
    • M/T car uses clutch-up switch.
    • Both connect to ECM E4 B13
  • Both the A/T and M/T switches get power from D/S J/B (different connectors – 1K vs. 1A) and relay through P/S J/B (different connectors – IG3 vs. IA1) before going to ECM.
  • Could wire clutch cruise switch in by connecting to wires at unused A/T conn P1, but it’s is on other side of firewall.

Summary of Modifications:

  • Removed clutch cruise switch connector and wires from M/T car.
  • Extended clutch-switch connector power lead (yellow/red wire) and spliced onto conn 1K pos 9 wire where A/T conn P1 gets power. (Since 1A and 1K both supply power the same way, no use in trying to use M/T-specific 1A connection. Used A/T power source 1K.)
  • Extended other wire from clutch-switch connector to get to P/S J/B. Spliced onto existing wire at conn IG3 pos 9 (where P1 connects), which connects to ECM E4 B13.
Clutch cruise-control switch (harness markup)
Wiring in the new M/T clutch cruise-control switch in place of the A/T shifter signal

Clutch cruise switch wiring


Snow/Trac Switch


  • M/T Snow button is positioned differently than in A/T car:
    • A/T Snow button is on shifter assy, and TRAC OFF is standalone switch under radio.
    • M/T Snow button is on combination switch with TRAC OFF button, together under radio.
  • Vehicles use different type of Snow and Trac Off switch types:
    • TRAC OFF switch on A/T car is 4-pin connector T7.
    • Combined TRAC/Snow switch is 6-pin connecor T14.

Summary of Modifications:

  • De-pinned black/yellow wire from A/T shifter conn E12 on top of trans tunnel.
  • Extended black/yellow wire to route up and around to new M/T Trac/Snow switch position under radio.
  • Took conn T14 from M/T car along with some black/yellow wire.
  • De-pinned TRAC OFF wires from existing (A/T car) 4-pin conn T7. Pinned into new T14 conn from M/T car.
  • Connected extended black/yellow wire into new conn T14 and new combined TRAC/Snow switch.

Snow and Trac switch wiring


Manual Trans Installation

I first did some prep work on the transmission:

  1. Clean the inside of the bellhousing (some kind of problem with the installed ACT 6-puck clutch caused it to shed all its friction material, leaving a thick coating of grease and dust everywhere).
  2. Burnish transmission input-shaft splines (to allow for a smoother engagement during install and hopefully less wear over time).
  3. Replace trans tailshaft seal (P/N 90311-38032).
  4. Grease release fork fingers, pivot, and input shaft
  5. Loosen trans fill bolt to make removal easier later when filling the gear oil.

I opted to use the lighter SC300 (W58 trans) single-mass flywheel over heavier W55 one used in manual IS300, and I bought an SC300 clutch kit to go along with it. This requires using a longer slave-cylinder pushrod as well. I used the Supra TT pushrod 31473-14030 (installed later).

I then prepped the engine side:

  1. Drain engine oil
  2. Replace the rear main seal (P/N 90311-90006)
  3. Install new pilot bearing in crankshaft
  4. Install flywheel
    • New ARP hardware from DriftMotion (for W58 since using SC300 flywheel)
    • Apply red loctite to bolts
    • Tighten to 75 ft-lb per DriftMotion
  5. Install clutch
    • Use clutch-alignment tool to keep clutch disc center in line with the pilot bearing
    • New bolts 90119-08026 (for SC300 clutch)
    • 14 ft-lb (FSM p. CL-14)
New clutch installed
New clutch installed

Next I installed the manual transmission in the car:

  1. Did not have to loosen engine mounts or lower the front crossmember. Lining up the input shaft was surprisingly easy.
  2. Plug in reverse-light switch connector
  3. Tighten bellhousing bolts (53 and 28 ft-lb, FSM p. MT-4)
  4. Re-install starter – 28 ft-lb (FSM p. MT-4)
  5. Rear mount/crossmember (19 ft-lb upper, 18 ft-lb lower, FSM p. MT-4)
  6. Install driveshaft
    • Center support bolts: 36 ft-lb (FSM p. MT-4)
    • Pinion-flange bolts: 54 ft-lb (FSM p. MT-4)
    • I retained the center-carrier spacers that the A/T car already had
FSM page PR-2 showing driveshaft spacers
Driveshaft center-support spacers (FSM page PR-2)
  1. Measure driveshaft angles.
    • Make sure engine isn’t jacked up anymore
    • Rotate driveshaft to settle
    • Raise and lower diff with jack to stabilize mounts
    • Angle specs on FSM p. PR-12
      • Center joint: -1.35° +/- 0.5°
      • Diff joint: +2.30° +/- 0.5°
    •  Measurements:
      • Front driveshaft section ~1.75° up
      • Rear driveshaft section ~2.75° up
      • Pinion 0°

FSM page PR-12 showing driveshaft angles


Center JointDiff Joint
Angle limits (FSM p. PR-12):-0.85° / -1.85°+1.80° / +2.80°


I did not install the sound/heat-insulation mat that lined the underside of the donor-car trans tunnel, since it was mounted using a lot of small M6 weld studs that are not present on the auto chassis.

I replaced the lower shift boot (33555-22130) from above once the transmission was in place. Installation involved applying oil to the inside of the rubber hole and shoving it over the shifter. It stretches a surprising amount.



I installed the clutch hard line and clutch slave cylinder, using the Supra TT pushrod 31473-14030 to get the extra length needed w/ the W58 clutch/flywheel combo. I greased the pushrod/release-fork interface and tightened the slave-cyl mounting hardware to 9 ft-lb (FSM p. MT-4). Both clip-in points for the hard line were present and un-occupied on the auto chassis, so I used those.

Supra TT (left) and standard W55 (right) slave-cylinder pushrods
Supra TT (left) and standard W55 (right) slave-cylinder pushrods

Then I added the trans gear oil. The capacity is 2.6 L/2.7 qt, and I used 1 qt of Redline MTL and Redline Lightweight Shockproof for the rest. I installed new crush washers 90430-18008 for the drain- and fill-plug bolts and tightened them to 38 ft-lb (FSM p. MT-11).

I then re-installed exhaust with these steps:

  1. Install manifold loosely with nuts (using new gaskets)
    • New gaskets
    • Put antiseize on nut threads
  2. Position jack to help with pipe install
  3. Install mid pipe and rear pipe
    • New gaskets 90917-06055 and 90917-06056
    • Put antiseize on nut threads
  4. Tighten manifold nuts: 29 ft-lb (FSM p. MT-3) – 30 per FSM p. EC-15
  5. Tighten exhaust flanges
    • Front exhaust flange: 46 ft-lb (FSM p. MT-4)
    • Middle exhaust flange: 32 ft-lb (FSM p. EM-62, FSM p. EC-15)
    • Rear exhaust flange: 32 ft-lb (FSM p. MT-4)
  6. Installed mid-pipe O2 sensor
    • Put antiseize on O2-sensor threads (sparingly)
    • Twist wire 3.5 turns left before installing
  7. Plug in all three O2 sensors

The trans exhaust mount from the A/T doesn’t fit the manual trans, so no exhaust mount installed. I couldn’t figure out what P/N the manual trans vehicle should use as an exhaust mount since the donor car had none, and the FSM and EPC seem to think auto and manual cars use same part.

I re-assembled other engine parts:

  1. Intake
  2. Re-connect upper rad hose, brake booster, other stuff that was disconnected to allow engine to tilt back.
  3. Fill coolant

Re-assembled interior:

  1. Install instrument cluster from the manual car
  2. Assemble shifter
    • Grease bushings
    • Bolt small flange to trans: 71 in-lb (FSM p. MT-3)
  3. Install parking brake
  4. Replace interior electronics and some trim

I re-fueled (after emptying during overfill check valve replacement), and finally, I double-checked everything visually and reconnected the starter battery.


First Start

With the major systems re-assembled, I tried to start the engine. It would crank but not fire.

The immobilizer system was preventing the car from starting since I had swapped over the donor car’s ECM (which contains the transponder-key registry). I expected that holding the donor-car’s key next to the ignition ring would be enough to deactivate the immobilizer, but apparently not; it doesn’t recognize a key unless it is plugged in. Since I replaced the ECM but not the ignition cylinder, I had one key that would deactivate the immobilizer but not turn in the ignition and one key that would turn in the ignition but not deactivate the immobilizer. Following the procedure on FSM p. BE-223, I was able to program my key as a new master key in the ECM.

I successfully test-started the engine. No leaks or other problems presented themselves.

I connected together the two ports on the A/T oil-cooler that sits in the bottom of the radiator to prevent leftover ATF from leaking out.

I bled the clutch line and the cooling system (FSM p. CO-2 – CO-3)

I checked the clutch-pedal adjustment (FSM p. CL-3)

  • Should release ~1″ above full travel
  • No adjustment needed.
FSM page CL-3 showing clutch-pedal adjustment
Clutch-pedal adjustment (FSM page CL-3)

I replaced the engine under covers, installed the wheels, and dropped the car.

After a short test drive in the neighborhood with nothing amiss, I replaced the rest of the interior trim.

I had mapped out every day of this project’s work over the preceding weeks to ensure it was finished on this day, since I had a powerlifting meet in Atlanta tomorrow, and I wanted to drive my car. So a few hours after finishing the two-month project, I set out on a two-hour drive.

On the drive, I encountered only minor irritations – the cruise control did not work, and the “Trac Off” light was constantly on. The reason for the first problem was the clutch cruise switch was loose and not actuating (even though I transferred it over as part of the pedal assy w/o touching the adjustment). Once I stopped and adjusted it, everything worked as normal.

IS300 wagon parked at Atlanta Barbell
Safely arrived in Atlanta

Through some research a few days later, I found that manual cars were not offered with VSC, and my A/T car did come w/ VSC. ToyoDIY shows 89540-53150 for manual car; shows 89540-53150 and 89540-53170 w/ VSC for auto car; shows buzzer and yaw-rate sensor as N/A for manual car. The skid-control ECU in VSC-equipped cars provides both traction control and VSC. This was confusing the manual (engine) ECM I was using, so I swapped in the manual donor car’s traction-control ECU, and that fixed the “Trac Off” light. The ABS actuator is also different between manual and auto cars, but unlike the skid-ctrl ECU, there are no pin conflicts (just added pins for now-unused VSC functions), so I kept the VSC version in my car.

It’s now been two years since the swap, and there have been no other issues.



Here I’ve transcribed all the references and notes I collected when preparing for and executing the conversion:

Diagnostic manuals ( thread)

Lexus Parts Websites ( thread) (parts lookup and illustrated parts breakdowns)

General Info + Where to Look ( thread)

Important LSD info ( thread)

Roughly 12% of IS300s have Manual Trans? ( thread)


ECU pinout

Vehicle manuals: 12345

Misc How-tos

Misc Install How-tos (ClubLexus thread)

Key programming ( thread) – Lexus-Toyota V8 Forum – Bedell IS300 1UZ S/C thread on

lextreme – Bedell IS300 1UZ S/C thread on Lextreme  

  • I first read about Brad Bedell in my MR2 days, and his 1UZ Sportcross swap thread was my first exposure to the Sportcross (and the 1UZ). – R154 – THE Ultimate Auto to Manual Swap Info Thread

  • Connectors from auto trans need to be spliced. – Auto to Manual Swap, Wiring, Ecu, CC, NSS, CLSW, Trac, Snow, now smogged in CA!

  • Wiring modification info
  • Lots of pics in this thread
  • Can get ECM re-seeded by dealership for ~$130.
  • Need to wire clutch switch to cruise control.
  • Need to extend snow button wires to get it to new button location.
  • Snow/ECT-Pwr button combo on shifter can be repurposed as snow/trac-off button with added benefit that now trac off will stay engaged since ECT Pwr is a latching switch.
  • Only consequence of using A/T ECU is CELs. Curran thought it drove better w/ A/T ECU. – How to manual swap and pass obd scanner

  • Manual ECU has a different harness than auto, so re-pinning necessary for ECU? [yes]
  • Can make auto ECM happy w/ some resistors according to Brad Bedell. – Converting 01 IS300 ECU to Manual

  • Does the immobilizer chip need to be moved? Part of ignition cylinder or ECU? – Manual Swap Options for $1800 Budget

  • Have to take dash out (for pedals?) [no – confirmed during swap]
  • Auto IS300s get speed signal from ABS sensors – 2001 IS300 auto to W55 swap! Need Help!

  • Info about speed input to ECM (01 and 02+)
  • ’02 Auto car:
    • ABS speed to cluster
    • Tailshaft to ECU [I think this is wrong based on FSM description]
  • ’02 Manual car:
    • Trans to cluster
    • Cluster to ECU
  • Can still get speed signal from ABS (more accurate because of using auto diff); rewire harness to send speed signal from cluster to ECU.
  • With manual cluster, it should have the right connections; the harness and ECU side just needs to change.
  • ’01 was never available w/ manual trans – my w55 auto to manual 5spd swap with 02+ wiring

  • Description of how to modify harness to send speed signal from cluster to ECU
  • Wiring pics – Manual conversion vs Engine conversion

  • Need to rewire neutral safety switch to clutch pedal instead of auto transmission. – Sportcross Story GTE AR5 Build – A Sportcross Story

Brake pedal assemblies are the same except for pedal arm itself. (ToyoDIY P/N comparisons)

Accel pedal assemblies are the same. Accel cables are the same. (ToyoDIY P/N comparisons)

MKIV N/A Supra/SC300 flywheel for W58 preferred because it is lighter and single-mass design with better feel. Need Supra or SC300 flywheel bolts (X8) 90910-02103 and slave cyl push rod (from TT Supra) 31473-14030. ( thread)

Need Supra TT slave cyl pushrod. Toyota flywheel bolts: 90910-02103 ( thread)

IS300 W55 flywheel bolts: 90910-02115

Supra TT pushrod: 31473-14030 (ToyoDIY) (ToyotaPartsDeal $7)

Supra flywheel P/N: 13405-46040. Supra TT pushrod is 81 mm. May want 82mm one if it chirps ( thread p. 3)

Another solution to chirping is using a spring to hold release fork so bearing is held away from hub springs. ( thread) – or away from the pushrod? ( thread). Some say to install pushrod backwards.

Clutch pedal adjustment ( thread)

Don’t need flywheel spacer that automatic has behind flex plate.

Flywheel torque spec ( thread)

ARP 203-2802 hardware works with W58 flywheel and IS300 engine. Use blue loctite. 70 ft-lb ( thread) – Gas tank/Fuel tank removal…Is there a DIY?!?

  • Unplug fuel pump before dropping tank
  • Disconnect anything accessible from top (sender, pump, and feed line)
  • 3 or 4 lines at the back of the tank need to be disconnected. (charcoal canister) – DIY walbro 255 fuel pump install with pics (alot)

What does Snow button do on manual car? FSM says it is part of electronic throttle control and is a more extreme traction-control application.

DIY: Immobilizer Hacking for Lost Keys or Swapped ECU by speedkar9 on Instructables

DIY: Odometer Reprogramming by speedkar9 on Instructables

Locksmith Charley Instructions for Programming Toyota/Lexus Keys – What Fails in the W55/W58 – Auto to Manual swap: parts, pics, prices, COMPLETED – Manual Swap: ECU question – IS300 Manual SWAP STEPbySTEP INSTRUCTIONS Ft. W58

Have to re-pair the key to the ECU when ECU is swapped. Could instead swap lock cylinders from manual car.

There appears to be an additional diff-mount cushion for M/T. – Question about manual lsd in auto IS300 – Is M/T drive belt tensioner needed for A/T->M/T swap – Trac Relay Removal

  • Speedometer signal comes from ABS module. If you remove power to that, you will not have speed.
  • On ’02+ manual-trans cars, there is a separate speed sensor in the trans. – Re-gearing Differential

  • Using speed sensor in manual trans with auto diff will result in incorrect speedometer output (reading slower). – How-To: ABS to Speedo Rewire for V160 swapped IS’s (02+ 5spd’s) – Clutch bleeding tips – Clutch swap DIY – IS300 How To Install a New Clutch (W55 or W58) – Transmission FAQ list

Toyota Wire Harness Repair Manual

  • Lots of useful cutaways of connectors and contacts which help with re-pinning.