DIY Auto-to-Manual Transmission Swap

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Old Mar 14, 2024
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Re: 03 civic ex transmission swap auto-manual

i did this, im using the auto dash harness but i did it the same exact way you did it, unfortunately im having an issue with no crank from the key, i ended up using the manual key switch just to see i got a click from the starter relay i jumped the starter and it somehow started on hopes and dreams im not getting any communication with the ecu though so im in need of help any advice you can give me on where to check what to check thanks. everything for the manual swap is from a 2003 honda civic ex and its all going into a 2005 honda civic special edition
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Old Mar 15, 2024
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Re: DIY Auto-to-Manual Transmission Swap

Check for blown fuses..
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Old Mar 15, 2024
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Re: DIY Auto-to-Manual Transmission Swap

Originally Posted by Colin42
Check for blown fuses..
ive tried unfortunately havent found any
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Old Mar 15, 2024
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Re: DIY Auto-to-Manual Transmission Swap

Checking with a meter or just looking?
if the alternator isn't grounded properly it can fry the ecu. Make sure all your grounds are clean and connected
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Old Feb 26, 2025
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Re: 03 civic ex transmission swap auto-manual

Originally Posted by 2002civicrider
Parts List:

Trans
Manual Subframe
Trans Mounts
Shifter
Shift Linkage
Master Cylinder
Manual Axles (You only need the drivers side)
Slave Cylinder
Pedal Assembly
Starter
Clutch
Flywheel
Manual Center Console (Or just the shifter bezel piece)

Not needed but nice to have:

Manual ECU
Manual Cluster
Manual Dash Harness
Manual Engine Harness

UPDATE: You do not need a manual engine harness. The manual ecu will work without it.

Time for swap: If you have general knowledge I'd say it should take you a weekend maybe a few extra days.. It took me a week because I couldn't figure out why it wasn't starting and I got screwed over by this ricer down in NC.

Note: I DO NOT take any responsibility for any injury's and or problems you have with your car during or after this swap. You are doing this at your own risk. I'll be more than happy to help you work out any problems you have tho.

First thing first. I did this swap with a manual engine harness, manual ecu, and auto dash harness. I recommend going this route because I personally think you will have a less of a headache and less chance of running into problems down the road.

Step 1: Put your car up on jack stands and remove the wheels and then drain all your fluids (oil, trans, and coolant), and uplug your battery.

Step 2: Go inside your car and remove the drivers seat, brake pedal, auto shifter, gauges (if you are putting in a manual cluster), and floor mats, glove box and auto ecu. The best way to get the ecu out is to drop the glove box, unbolt the metal support and cut the plastic piece so you can bend it out of the way.



Step 3: Now you want to go to the engine bay. Start removing the header, intake, p/s pump, alternator, remove the battery and battery tray, throttle cables off the tb, remove the radiator, ac condenser, bumper support, and pull your axles.. all that good stuff . That's basically it.. There's probably a few other things I have forgotten but you'll see them when you are in there. Don't forget to unhook the auto shifter linkage. We forgot to and it snapped while pulling the motor.. No big deal .



Step 4: Now go into the engine bay. Start unhooking your engine harness. Once most of it's unplugged you should have almost the whole harness on the passenger side of the car. You should've already unplugged the ecu in the previous step so now you want to pull the connector's thru the grommet and then the harness should be removed from the car. Also this would be a good time to pull your injector rail out as well since you are in that area. The fuel rail can be a pain the first time if you haven't removed it before. Here's a good technique:



And here's a picture with the harness moved out of the way: (This pic will be used twice)



Step 5: Now it is time to start pulling the motor. Engine hoist is recommended for this step. It will make your life so much easier. You will need to find 2 places on the motor to hook up to the hoist.



Once you have the motor held by the hoist you can start taking the motor mounts off. Once you get all the mounts out carefully lift the motor out of the car.



Now you are halfway there!

Step 6: Get the motor on the ground so you can pull the crappy auto trans off the motor . Now would also be a great time to clean that motor and engine bay with the motor out. Once you get the auto trans off you need to remove that pos torque converter off. Now you are left with the motor. Go grab you flywheel and clutch and install onto your motor. Make sure the clutch is aligned before moving on.

( This pic will do for now. We were comparing the a/t flywheel bolts vs the m/t flywheel bolts)



Step 7: Get under the car and unbolt your auto subframe. Drop the bitch out and reinstall the manual. Pic!



Step 8: Now it's time to mate that awesome manual transmission up to your motor. Once you get the trans mounted get everything back up on the hoist and drop her back in. Here's a pic of it installed:



Step 9: Now would be a good time to run your clutch hardline since you don't have everything in the way. You will need to remove the cruise control box to run this behind it. Here's some pics of how mine is ran:









Step 10: Now what you want to do is run your engine harness. Run the pin portion threw the grommet towards the ecu and then start running the harness throughout the motor. Once the harness is done you want to start installing your header, intake mani, p/s pump, alternator and all that other stuff you removed in step 3. Now your motor should almost complete.



Step 11: Now get in your car and drill out the hole for the clutch and bolt it up. (No pic of this) It's pretty straight forward. Honda has a imprint in the firewall where you need to drill out at. Also bolt your brake pedal up as well since your are down there.

Step 12: Now comes the small amount of wiring you need to do. You need to unbolt the 10mm bolt that holds the underdash fuse box up and drop it all the way down. Here's a picture of the diagram:



Now what ur going to do is, is go up under the dash on the drivers side. Ur gonna want to locate the fuse box. There's a 10mm bolt and unbolt it so the fuse box will move down to where u can access towards the top. Next, your going to want to locate connector D. If i recall it's located in the middle on the 2nd row from the top. Don't quote me on that one. Once u find this connector, pull it out. Then locate pin 7 (Lt. Green) and pin 10 (Blue/Black). Come out from the fuse box a little and cut both of them. Now what your going to want to do is put the connectors with a loop on the end on all 4 so u can run a bolt thru them. Find urself a grounding point, and ground all 4 wires out at the same point. Just do this so u don't ground out the half of the wires as i did and didn't discover for 6 months. Afterwards, connect ur battery and when u turn the key on the P should b lite up (If you are running the auto gauge cluster). This will allow the car to start after this swap.

Step 13: Now you want to install you awesome shifter box. I suggest buying the strut king shifter cable and base bushing. You can get them from Corsport for pretty cheap. I also recommend the revo ss shifter as well. 89 shipped from Clubrsx when I bought it. Now hook up your shifter cables to the shifter. You can hook up the cables to the trans itself now if you didn't already. Also be sure to bolt the cables to the undercarriage. There's a spot on the chassis. You will see it when you are under there.

Step 14: Finish installing all your interior back together. Hook up your ecu as well. Before putting the glove box back this would be a great time to wire up your reverse lights.

Step 15: Now that your interior is complete all you really need to do is fill up all your fluids... Oil, Trans fluid, and coolant and hook up your battery.

Step 16: Now go back and double check everything. Make sure everything is tight, plugged in and ready to go. Now is the time for truth. Get in your car and see if it starts. If it does give yourself a pat on the back for a job well done.

Hopefully this helps you out.
Okay so phenomenal write up thank you very much sir! I know this is a really old thread but if you are here in 2025 a few things to note. I noticed first off flywheel bolts are different (very important). You need the passenger side axle if you have an aftermarket axle which in 2025 you probably do your (CV axle will fall out). And last I recommend going and watching Eric the car Guy clutch replacement video and it will teach you everything you need to know about the actual removal of the transmission.
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Old Mar 30, 2025
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Re: 03 civic ex transmission swap auto-manual

Originally Posted by 2002civicrider
Parts List:

Trans
Manual Subframe
Trans Mounts
Shifter
Shift Linkage
Master Cylinder
Manual Axles (You only need the drivers side)
Slave Cylinder
Pedal Assembly
Starter
Clutch
Flywheel
Manual Center Console (Or just the shifter bezel piece)

Not needed but nice to have:

Manual ECU
Manual Cluster
Manual Dash Harness
Manual Engine Harness

UPDATE: You do not need a manual engine harness. The manual ecu will work without it.

Time for swap: If you have general knowledge I'd say it should take you a weekend maybe a few extra days.. It took me a week because I couldn't figure out why it wasn't starting and I got screwed over by this ricer down in NC.

Note: I DO NOT take any responsibility for any injury's and or problems you have with your car during or after this swap. You are doing this at your own risk. I'll be more than happy to help you work out any problems you have tho.

First thing first. I did this swap with a manual engine harness, manual ecu, and auto dash harness. I recommend going this route because I personally think you will have a less of a headache and less chance of running into problems down the road.

Step 1: Put your car up on jack stands and remove the wheels and then drain all your fluids (oil, trans, and coolant), and uplug your battery.

Step 2: Go inside your car and remove the drivers seat, brake pedal, auto shifter, gauges (if you are putting in a manual cluster), and floor mats, glove box and auto ecu. The best way to get the ecu out is to drop the glove box, unbolt the metal support and cut the plastic piece so you can bend it out of the way.



Step 3: Now you want to go to the engine bay. Start removing the header, intake, p/s pump, alternator, remove the battery and battery tray, throttle cables off the tb, remove the radiator, ac condenser, bumper support, and pull your axles.. all that good stuff . That's basically it.. There's probably a few other things I have forgotten but you'll see them when you are in there. Don't forget to unhook the auto shifter linkage. We forgot to and it snapped while pulling the motor.. No big deal .



Step 4: Now go into the engine bay. Start unhooking your engine harness. Once most of it's unplugged you should have almost the whole harness on the passenger side of the car. You should've already unplugged the ecu in the previous step so now you want to pull the connector's thru the grommet and then the harness should be removed from the car. Also this would be a good time to pull your injector rail out as well since you are in that area. The fuel rail can be a pain the first time if you haven't removed it before. Here's a good technique:



And here's a picture with the harness moved out of the way: (This pic will be used twice)



Step 5: Now it is time to start pulling the motor. Engine hoist is recommended for this step. It will make your life so much easier. You will need to find 2 places on the motor to hook up to the hoist.



Once you have the motor held by the hoist you can start taking the motor mounts off. Once you get all the mounts out carefully lift the motor out of the car.



Now you are halfway there!

Step 6: Get the motor on the ground so you can pull the crappy auto trans off the motor . Now would also be a great time to clean that motor and engine bay with the motor out. Once you get the auto trans off you need to remove that pos torque converter off. Now you are left with the motor. Go grab you flywheel and clutch and install onto your motor. Make sure the clutch is aligned before moving on.

( This pic will do for now. We were comparing the a/t flywheel bolts vs the m/t flywheel bolts)



Step 7: Get under the car and unbolt your auto subframe. Drop the bitch out and reinstall the manual. Pic!



Step 8: Now it's time to mate that awesome manual transmission up to your motor. Once you get the trans mounted get everything back up on the hoist and drop her back in. Here's a pic of it installed:



Step 9: Now would be a good time to run your clutch hardline since you don't have everything in the way. You will need to remove the cruise control box to run this behind it. Here's some pics of how mine is ran:









Step 10: Now what you want to do is run your engine harness. Run the pin portion threw the grommet towards the ecu and then start running the harness throughout the motor. Once the harness is done you want to start installing your header, intake mani, p/s pump, alternator and all that other stuff you removed in step 3. Now your motor should almost complete.



Step 11: Now get in your car and drill out the hole for the clutch and bolt it up. (No pic of this) It's pretty straight forward. Honda has a imprint in the firewall where you need to drill out at. Also bolt your brake pedal up as well since your are down there.

Step 12: Now comes the small amount of wiring you need to do. You need to unbolt the 10mm bolt that holds the underdash fuse box up and drop it all the way down. Here's a picture of the diagram:



Now what ur going to do is, is go up under the dash on the drivers side. Ur gonna want to locate the fuse box. There's a 10mm bolt and unbolt it so the fuse box will move down to where u can access towards the top. Next, your going to want to locate connector D. If i recall it's located in the middle on the 2nd row from the top. Don't quote me on that one. Once u find this connector, pull it out. Then locate pin 7 (Lt. Green) and pin 10 (Blue/Black). Come out from the fuse box a little and cut both of them. Now what your going to want to do is put the connectors with a loop on the end on all 4 so u can run a bolt thru them. Find urself a grounding point, and ground all 4 wires out at the same point. Just do this so u don't ground out the half of the wires as i did and didn't discover for 6 months. Afterwards, connect ur battery and when u turn the key on the P should b lite up (If you are running the auto gauge cluster). This will allow the car to start after this swap.

Step 13: Now you want to install you awesome shifter box. I suggest buying the strut king shifter cable and base bushing. You can get them from Corsport for pretty cheap. I also recommend the revo ss shifter as well. 89 shipped from Clubrsx when I bought it. Now hook up your shifter cables to the shifter. You can hook up the cables to the trans itself now if you didn't already. Also be sure to bolt the cables to the undercarriage. There's a spot on the chassis. You will see it when you are under there.

Step 14: Finish installing all your interior back together. Hook up your ecu as well. Before putting the glove box back this would be a great time to wire up your reverse lights.

Step 15: Now that your interior is complete all you really need to do is fill up all your fluids... Oil, Trans fluid, and coolant and hook up your battery.

Step 16: Now go back and double check everything. Make sure everything is tight, plugged in and ready to go. Now is the time for truth. Get in your car and see if it starts. If it does give yourself a pat on the back for a job well done.

Hopefully this helps you out.
can u help me with the pics
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