Auto to Manual Trans ''How to'' guide

Looks like my auto trans is done and I might end up going this route

Always wanted a 5 sp, but not necessarily now

MY SWAP IS DONE! I did it over Thanksgiving weekend. It took me and my dad two full days of work, from sunrise to sunset. it was def. worth it. shes running like a champ! i did it with the help of this write up and one from this website Auto to Manual Swap - The Mustang Collective Forums also the service manuals on the top of that post helped alot. I want to thank you anthony your write up was very help full also to temugen from the mustangcollective.
If anyone has any questions or need adivce about the swap id be happy to help. To anyone thinking about doing it, its not hard but you need to be some what mechanically inclined. any DIYer with the right amount of research can do it.
just giving back to the community.

Sure glad this is stickied will be tackling this in the near future.

can you post pictures on how to put the clutch pedal in???

Dan Harper said:

can you post pictures on how to put the clutch pedal in???

Click to expand...

It goes in just like the brake pedal assembly for the auto came out. Only this time the back part of the clutch pedal side goes through the hole in the fire wall.

Is it just easier to swap harnesses out or to modify the existing one? I'm having issues locating a manual PCM :/ Can anyone point me in the right direction on the electrical side of things. I'm worried about losing my cruise control and the whole brake light fiasco. I have a 2006 GT auto.

Just follow the write up. Either way you go with the harness your gonna lose cruise control, I havent found anyone who has been able to get it to work.

Quick question. Do I need a new crossmember for the 3650 or will the one for the 5r55s be able to be reused?

Justinsmt88 said:

Quick question. Do I need a new crossmember for the 3650 or will the one for the 5r55s be able to be reused?

Click to expand...

You can reuse the same cross member. I actually did this swap last fall, thanks to Anthony's write up. As a note, I've got an '06 and I replaced the wiring harness and pcm from another '06. It did require a tune to get it working properly, but no issues and with proper tools and a lift, I was able to complete the swap in a day.

Thanks for leading the charge on this so many years ago Anthony

Question for anyone who replaced the harness and computer. How and where do you hook up or bypass the clutch position switch? I cant locate the wiring for it an have had to start my car by jumping it in the fuse box every time I want to start it.

were you able to get cruise control to work?

Could you possibly take some pictures to show me what you are talking about and or what wires to connect?

Transmission went out yesterday need some guidance and the neutral safety switch. i read the plug is under the dash (mines an 06) anyone have the part number the wiring harness? Im still gathering the little things

eddieval5 said:

Transmission went out yesterday need some guidance and the neutral safety switch. i read the plug is under the dash (mines an 06) anyone have the part number the wiring harness? Im still gathering the little things

Click to expand...

Normally there may be a connector up under the dash probably above the brake pedal or clutch pedal location, you may not see it but it should be there, what I would do is use a flash light and look for a black bundle looks like black foam tape, on the 10-14s S197s it is wrapped up with a black very sticky tape off another connector. It could be located on the side of a larger connector up there too. It will be very obvious. Check each bundle you see but it should be around that location just follow the other wires in there. (on 2010 and newer it is connector # C215) I am not sure about 05-09s.

Regarding 05-14 S197s PCM etc. The CPP and cruise control deactivation harness (neutral safety switch if you will) needs to be used if you want to make use of the factory setup, however you will still need your PCM either tuned, or reflashed by ford. According to my sources you cannot reuse the MT PCM if you swap a T5 or MT82 or whatever to an AT transmission you will need the PCM from the AT. However if you are going from AT to MT you can re-use the AT PCM. You will need to have Ford or someone with IDS to re-program the PCM as a MT unit (initialize it as a manual transmission vehicle so it knows what controls to use) and flash it with the correct MT strategy code, as built data, your vehicle info (VIN# and mileage) and program two car keys for PATS(so the car will start). You can also just get a MT PCM and have them just do the flashing of the correct MT strategy code(if needed but should not be), as built data, your vehicle info (VIN# and mileage) and program two car keys for PATS.

If you do not use the CPP/Cruise disable jumper, the MT wire harness, and a MT PCM or reprogrammed PCM initialized as a MT the PCM though module communications network, other components will not know how to use the reverse lights or cruise control or neutral lockout features. For example my car I swapped out my 6R80 auto for the MT82. I had the PCM retuned so the car runs but the PCM is still looking for a signal from pin 39 on the upper plug of the PCM harness to tell the body control module to complete the circuit to turn on my reverse lights. However since I am running the MT harness now there is nothing on pin 39 the reverse switch is actually now on pin #17 which the PCM does not know about and is not programmed to do anything with it. This is because it is still initialized as an AT transmission vehicle. When you reinitialize it and tell it that it is a MT it will properly function as it should as far as to look for a signal on pin 17 now and then will communicate with the rest of the network through the can bus and tell the BCM that it can turn the light on with the switch is closed. Same deal with the cruise control as it does not know how to communication with the transmission now for things like speed etc since the auto was removed. It also needs to know there is a clutch pedal switch now too.

Usually the easiest thing to do it replace the PCM if you do not want to wire up fixes. A good tuner may be able to get everything going but replacing or re-configuring the AT pcm is the way to go.

According to the workshop manual 05-09 does use the same connector for the Clutch pedal for neutral lockout and cruise control deactivation on connector C215 under the dash board, see pic below for location to look... (it is a rough location but its there.)

3.7cyclone said:

According to the workshop manual 05-09 does use the same connector for the Clutch pedal for neutral lockout and cruise control deactivation on connector C215 under the dash board, see pic below for location to look... (it is a rough location but its there.)

Click to expand...

BTW the pigtail that plugs into C215 also goes to C277 and C257 which are the switches on the clutch pedal. It is the same setup as the 10-14s.

3.7cyclone said:

BTW the pigtail that plugs into C215 also goes to C277 and C257 which are the switches on the clutch pedal. It is the same setup as the 10-14s.

Click to expand...

I did the swap a few years ago and I haven't had any problems. I replaced the old AT PCM for a MT PCM, reused the existing wiring harness w/modification of course, but I never installed a neutral safety switch. If I were to install a neutral safety switch would I be able to use cruise control or is there something else I need to modify? Great info that you've provided by the way.

I replaced my automatic transmission with a tr3650. I installed the harness for the clutch pedal, used an aluminum flywheel and after market shifter. I am still using the automatic ecm and wiring harness with the changes from this post. I have had the car at Ford and they couldn't get the ecm reflashed. They said I have to get a Manual Transmission ecm and have it flashed.
I took it to a local tuner and had a tune put in via my SCT hand held. None of the auto trans codes come up but the spedometer doesn't work and 2 other codes come up. The engine won't Rev past 4000 rpm. Any suggestions?