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DIY: Auto to Manual Swap (The long awaited)

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    • Edited 2 times, last by tunertc18 on .
    So many of you saw my thread about completing this overwhelming task, etc… I was asked to do a writeup and/or DIY. One small problem, I didn’t take many pictures so it will be a mostly written DIY. But here it goes:

    Here's my parts list:

    Manual Transaxle complete assembly
    Manual Transaxle Seal Kit (for axles)
    Clutch Flywheel Bolts(Manual)-8
    Clutch Flywheel
    Clutch Pressure Plate
    Clutch Pressure Plate bolts (6)
    Clutch disc
    Clutch Master Cylinder
    Clutch Pedal Top Bolt and Nut
    Clutch/brake Fluid Reservoir (manual)
    Clutch Fluid Reservoir hose to master cylinder and hose clips
    Manual Brake Pedal
    Manual Clutch Pedal
    Clutch Slave (release) Cylinder
    Clutch Slave cylinder bolts
    Clutch Master cylinder nuts (to firewall) (2)
    Clutch Master cylinder gasket
    Clutch Release (thrust) Bearing and clip
    Clutch release fork and boot
    Hydraulic Line #1 (Master Cylinder to Flex hose; AKA the one mounted to the master cyl.)
    Clutch Line flex hose
    Clutch flex hose Brackets (2 different) with necessary hardware
    Hydraulic Line #2 (Flex Hose to slave cylinder; AKA the one mounted to the slave cyl.)
    Manual Motor mount bracket Rear and bolts
    Manual Motor mount bracket Left (driver’s) Side and bolts
    Manual ECU
    Manual Engine wire Harness
    Shifter linkage with necessary clips
    Shifter linkage bolts (3)
    Shifter linkage bracket (underside)
    Shifter linkage Bushings
    Shifter cage with knob
    Manual shift boot

    You do not need:

    Manual axles (the auto ones will work), gauge cluster, manual ECU or harness (I didn’t want a CEL so I HIGHLY recommend getting it).


    • At least 36 hours
    • A friend or two to help
    • 30mm 12 point Deep well socket (For axle nuts)
    • Ratchet Bar for sockets
    • Socket set (Metric) I used 3/8” drive; make sure the following are included:
    • 8mm socket
    • 10mm socket
    • 12mm socket
    • 14mm socket
    • 17mm socket
    • 3”, 6” and 12” socket extensions
    • Universal Joint
    • Breaker Bar(s) (I used ½” drive)
    • Torque wrench
    • 8,10,12 and 14mm Gear wrench/open ended/combination
    • High temp grease/ Axle grease
    • Plenty of muscle
    • Philips screwdriver
    • Flathead screwdriver (Multiple sizes will help)
    • Set of allen keys (to drain the tranny fluid) (10mm)
    • Hydraulic floor Jack
    • Jack Stands (4)
    • Dead Blow Hammer
    • Adjustable wrench
    • Fluids drain pan
    • Prybar/crowbar
    • Knock out punch set (electricians tool)
    • 90 degree angular drill
    • Unibit (For pilot hole in firewall for clutch pedal)
    • Small piece of wire
    • Soldering iron, solder and flux
    • Tape
    • Goggles
    • Sharpie
    • Small block of hardwood (1”x2”x5”)


    1. Jack up the car and put it on 4 jack stands. You’ll want to make sure it’s pretty high because you will have to slide a tranny out from underneath. Under the car, remove the exhaust heat shield separating the midpipe from the body of the car. There are 3 nuts connecting it. I also removed my S-Pipe to make it easier to access certain bolts. Also break the front lug nuts before raising the car.

    2. I started with the interior disassembly. You DO NOT need to take off the dash. I removed the glovebox, waterfall/shifter assembly, cupholder and radio. In the engine bay, remove your intake, battery, and battery tray.


    3. After the above are removed, take your ratchet and start to disassemble the shifter assembly inside. There are 4 bolts holding it to the chassis in the center console area. Then you need to disconnect the cable from the assembly. Pull out the shifter, and you will have some room to work with.


    4. Next comes the actual linkage. To get to the bolts holding it in, you must remove the airbag control module. This is all on the inside of the car. It is the little silver and green box above the shifter linkage. There are 3 bolts and one plug connecting it. Remove it, and now you can access the linkage bolts. There are 2 bolts that hold the linkage plate (and linkage with rubber square thing) to the chassis. Reach your hand with a 12mm wrench up the linkage from the inside and under the insulation under the heater core, remove the 2 bolts. Then on the underside there is a bracket and one bolt securing the linkage to the car body. Once removed, disconnect all linkage retaining clips and remove the assembly where it bolts to the tranny. Once everything is removed, pull the linkage out through the engine bay.


    5. Next step is to begin disconnecting the wiring harness. This step is pretty straightforward. All of the clips that are connected to it and the car just unclip, same with the bolts. You can use your new harness as a guide to see where all the clips are. The only tricky part to this which took me about 2 hours is the part of the harness that runs through the intake manifold. You need to remove the 5 bolts connecting it (the manifold) to the engine, and it will slide down out of your way. There are some clips holding it in, but once those are removed, the harness will be fully disconnected in the engine bay. I did this step after the tranny was out because it was easier to access, (and put the block of hardwood under the engine in between the crossbrace supporting it. This will allow you to swivel the engine forward and gain better access to the manifold), but it’s personal preference. On the inside, remove the ECU. It’s located on the passenger side behind the glovebox. It has 1 bolt and a Philips screw thing holding it in. Disconnect all connectors/plugs and the wire harness should pop out through the firewall on the same side. Pull through from engine bay. While the intake manifold is out of your way, install the new harness and all connectors. Then re-bolt the intake manifold to the engine and the rest is self-explanatory. Connect all clips and plugs, etc… Pop the new harness through the firewall as well. You will want to re-bolt the new manual ECU in too and then plug all the new stuff back in.


    6. Next on to the axles. After your rims are removed, there is a 30mm 12 point axle Hub nut. It is screwed on and then has a pinch in it to hold in place. Put a screwdriver under the pinch and try to pry it out. Then just break the nut loose and set aside. Also remove the ABS sensor bolt. It secures the sensor to the hub assembly. You can recognize it as the black and blue thick wire that runs up the strut assembly. Be careful with that and hang it elsewhere. Now looking under the car up behind the rotor, there are 2 nuts and one bolt holding part of the cross member to the Hub assembly. Remove these and pull the hub assembly up and away, out of the axle. This goes for both sides.


    7. Now go ahead and drain the tranny fluid. It is the black box under the tranny with a hex bit (allen key). Remove and drain.

    8. Passenger axle: There are 2 bolts in the middle of the axle holding this assembly to a “frame” connected to the engine. They are in the middle of the axle, one on top and one on bottom. Remove them, and then tap the frame a few times and pull the axle out of the tranny.


    9. Driver’s axle: Looking up from underneath, on the axle assembly by where it connects to the transmission, there are little grooves on it going around. You have to stick a crowbar in one of them and basically pry the axle out. If you absolutely cannot get it, you can drop the tranny ONLY with the driver’s side axle still connected.

    10. Before you drop the tranny, look under the car from the passenger side towards the driver side. There is a plastic plate on the tranny above the cross member in the front. Remove that, and there are 6 bolts connecting the torque converter to the flex plate. THESE MUST be removed before the tranny is removed. What you need to do is rotate the flex plate by turning the crank pulley bolt. As it rotates, remove the 6 bolts through the access port where the plastic plate was, and set aside. I don't have pictures of this unfortunately.

    11. Also, you need to disconnect the 2 coolant lines connecting from the radiator to the tranny. Unscrew them from the tranny and disconnect from the radiator. What I did here was connect the 2 ports coming out of the radiator so nothing would leak. I used one of the soft hoses from the line(s) and clamped it to each end.

    12. Now on to actually dropping the tranny. There are a series of bolts that go around the tranny bolting it to the engine. They are pretty noticeable. I’m not sure exactly how many there are, but remove them. Once unscrewed, remove the long bolt for the rear motor mount that connects the mount to the bracket, and same for the driver’s side mount and front mount. Place the jack under the tranny to support it and make sure all bolts and clips are removed. The tranny will start to move and wiggle it away from the engine. Slowly lower it down and the torque converter will fall out. BE CAREFUL when dropping the gearbox as it is TWICE as heavy as the manual.


    13. Once that is out, you will want to remove the flex plate. It is bolted to the engine with 8 bolts in a circle and looks like a flywheel, but for the automatic. Remove that and set aside. You will NOT need the thin metal spacers on the front and back of it.

    14. Now go ahead and transfer all of the necessary hardware and brackets and starter to the new manual transmission (or whatever is missing.) Also, install the new axle seals to the tranny. Use grease.

    15. Since you have some more space to work with now, this is when I drilled the clutch pedal hole in the firewall. Have someone from the inside of the car, using the master cylinder gasket as a template, mark the holes on the firewall where the clutch pedal will go. There is a cutout in the dampening material that gets removed. It can’t be missed. You will also want to remove the seat since it’s only 4 bolts and gives you much more room to work with.


    16. Now, still on the inside, use the unibit and drill to drill the 2 “corner” holes (from the master cylinder) to their proper size. Drill the center hole (where the pushrod goes through) as big as possible. I used the knock out punch set to make the center hole the proper size. I also made them a bit bigger than needed so it could get set into place easier.

    17. Before you install the clutch pedal, you need to swap the brake pedals. I 100% recommend that you just swap the arms as the entire assembly swap is unnecessary. There is one “through” bolt holding the arm and a cotter pin and clip. Remove these, and swap the brake pedal arms.


    18. Now you can install the clutch pedal. Have one person hold the clutch master cylinder from the engine bay while you slide the clutch pedal assembly in place. The gasket goes on the outside of the firewall. Bolt down the 2 “corner” nuts to the master cylinder and clip in the pushrod and cotter pin. Now comes the tricky part. There is a THIRD top bolt that holds in the assembly. You can look at the brake pedal as a reference but you will notice it (the bracket). What you need to do is take the bolt and nut meant for it and tighten them down so that the clutch pedal is fully secure.


    19. Before installing the tranny, you need to install the flywheel, pressure plate and clutch disc. The flywheel sits where the old flex plate thing was (without the spacers) and make sure you use new manual flywheel bolts (. Then you have to put on the clutch disc and cover it with the pressure plate. Use the alignment tool and make sure it is in the center for the spline drive to slide in. There are 6 bolts on the circumference of the pressure plate that hold it in place.


    20. This next step I did before installation of the transmission. Screw in one of the hydraulic lines (The long one with many bends) to the clutch master cylinder and connect it to all brackets and clamps running on the side of the chassis. It will fall into place. Also install the flex hose bracket to the chassis. It is held in by one bolt and attaches to the frame just under the radiator.

    21. Now it’s time to install the transmission. OHHHH BOY. Place it on the jack and align it under the car. Slowly jack it up and into place. Getting the motor mounts and brackets in is quite the trick. What I did was remove all brackets, get the tranny in place and then bolt it too the physical engine. After it was bolted, I bolted the rear, side and front mount brackets to the actual transmission. The side is easy to then install the mount to, but the front and rear MOUNTS (what bolts to the chassis) might need to be removed to secure the bracket to the tranny. Then install all the long “through” bolts connecting the bracket and the mount and you’re good to go. I ran into a MAJOR problem with my front mount as I actually stripped the threads that the bolt screws into inside the tranny. I had to re tap and helicoil the tranny. Be CAREFUL!!!

    22. Next install the axles. The passenger axle should slide right in, also use a bunch of grease. MAKE SURE THAT THE SPLIND DRIVES ARE LINED UP. Re-bolt the 2 intermediate assembly bolts and then assemble the axle hub assembly. Re secure the cross brace to the hub assembly with the 2 nuts and 1 bolt. The driver’s axle also just pops right in. It may take the dead blow hammer to get in, but make sure the splines are aligned and use muscle. Then once again, re install the hub assembly and cross brace. Then go ahead and tighten the hub nuts on each side. They tighten to 159 ft lbs, but make then as tight as possible.


    23. Plug in the wire harness plugs to the corresponding plugs on the transmission. Also make sure the slave cylinder and flex hose bracket #2 are bolted to the transmission.


    24. Install the second hydraulic line and clamp (the one that screws into the slave cylinder and connects to the flex hose; AKA the small one). Then screw the flex hose into both ends of each hydraulic line and use the slide clips to hold it to the brackets. To complete the clutch system, you need to swap the brake/clutch fluid reservoirs and reconnect brake lines. Plug back in the brake lines fast and don’t let air get into the lines so that you will not have to bleed the system later. Then connect the piece of tubing from the third point on the reservoir to the point on top of the master cylinder. Secure with the included squeeze clamps. Pour in DOT 3 brake fluid in the reservoir. I then bled the clutch pedal. It is simple to do but if you need help look online.

    25. Back to the inside of the car, take the new shifter linkages and slide them through the firewall. Connect the brackets together on the underside of the car and then re-bolt those 2 bolts that secure the plate (rubber with metal plate on top) from the inside. In the engine bay, connect the other end of the linkage to the tranny and use the slide in clips to attach the cables to the bracket. This is also where your cable bushings go. Once that is secure, go back to the inside and re install the airbag control module. Snug it down tight and plug in the wires. Next secure the linkage in to the shifter cage (the big plastic piece with the knob). Shoot me a PM if you don’t know how too. Then bolt down the cage (using the same auto bolts) to where the auto one was.


    26. You’re going to need to replace the tranny fluid at this time. Check out guides online of how to do this, but it is fairly simple. It takes 2.5 quarts.

    27. At this point, you should have a bunch of cuts on your hand but be thankful that all the hard work is FINALLY DONE!!!

    28. Back to the engine bay, reinstall the intake, connect the MAF sensor and re secure the battery tray and battery. Finish connecting all wires and plugs in place, and connect the battery wires. Now, in order to make the car start, you have to re learn the ECU since it has been replaced. I AM NOT SURE IF THIS IS FOR THE AUTO HARNESS/ECU. Before you do this, in the fuse panel in the engine bay, the part with all the wires that is connected to the actual harness, there will be a purple and black relay. On the underside (opposite side of the relays) there will be 2 thin black wires (lead to same port) and one thicker blue wire. They each lead to one of the 4 terminals on the purple relay. You need to splice the black wires with the blue wire in order to bypass the clutch start switch. What I did, which is the clean and smart way to do this, is to short out the corresponding 2 “prongs” on the purple relay. I will show you which ones. Pull the relay out, and use the small piece of wire and solder it to each of the prongs, shorting out the circuit. Then plug the relay back in. You need to be sure to not start the car in gear, or push in the clutch if you do! Next step is resetting the ECU. Take a regular paper clip and bend it into a “U” shape. You need to short out the TC and CG pins on the OBD2 port. Plug one end into each port. Then turn your key to the “on” position, not started, and let the car sit for 35 minutes. Your dash lights will be going crazy, but that’s normal. After the time is up, take out the key, pull out the paper clip, and then start the car. Mine started right up. Then reset your windows and sunroof and radio presets.


    29. Re install the seat, waterfall assembly, radio, glovebox and anything else you removed. Let it idle for a while and make sure it drives smoothly. Re check all your connections and you’re set. Now go out and drive! REMEMBER... no hard shifts or pulls for the first 500 miles because you need to go very easy on the clutch and break it in.

    I’d like to say a big thanks to shane_rhabb and simplyibet on Scionlife for being such a great help all this way and potentially being my lifelines! Also I’d like to thank my dad for helping me along this difficult journey. Remember, I am not responsible if you mess up your car in any way, but I am always here to help. My phone number is 954-551-0394 or you can PM me. I hope every tC owner gets to enjoy this DIY and I hope to get known better around the scion community for this!
    Awesome! great job man.
    Nicely done. I am impressed that you got it done in the house gaarage, I dislike doing trani work that close to the ground.
    I enjoyed reading it.
    Thanks haha thats good to hear
    Nice DIY, really well written. Should be helpful for anyone else wanting to do the swap. Did you use an OE clutch and flywheel or aftermarket and lightweight?
    I used an aftermarket stage 2 clutch and 12lb flywheel
    I am in the process of swapping now. I got the tranny out and now I have to get the torque converter(i think) out. It does not just "fall out" like you said. mine is bolted on through the flex plate. My question is how do I take it off so i can get the flex plate off? I am not to familiar with auto trannys. I just got the auto tranny out and this is my next step towards getting the new one in. I have everything needed to complete it just need help with this. Any help would be great.
    I know this is 8 years old, just out of curiosity (ball park) what did this cost?
    What was the cost for all the parts in the end of this and who do you recommend getting all the parts from
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