Auto to Manual Trans ''How to'' guide

x_doug_x

New Member
Aug 1, 2012
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0
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36
I am having a buttload of issues and have a few questions, number 1. if i'm not going to use reverse lights, can I just pull the bulbs out? The tuner I have sending a tune said reverse lights will be on all the time. Second question, Can the clutch switch stay jumped out or does the pcm have to see a clutch input? I bout one of the 2 manual pcms (there are 2 for a 06) off ebay, installed it and it kept blowing the pcm fuse. I re-installed my pcm and paid someone to send me a manual tune. They have sent me 4 or 5 now, the car will only run with a auto tune. When flashed with a manual sometimes it starts up and shuts off, most of the time it won't start at all. According to the tuner viewing the datalog the pcm is in fuel cut, need to know if anyone can give me some tips or let me know what I can do to get this car running like it's suppose to. I am unsure if it's something i've done or the tunes themselves.
 
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x_doug_x

New Member
Aug 1, 2012
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36
I would also like to add 2 more things, car will start fine with the factory auto tune, will not start with a manual strategy tune. I also do currently have a clutch safety switch hooked up (wanted to know for my own piece of mind) and it's also throwing codes p0690 and p0685(only with the manual strategy tunes). I have googled and read all about these codes, swapped pcm power relays, just not really sure what's going on.
 

sosocrates

New Member
Aug 29, 2021
4
0
1
18
USA
On post #11, Anthony talked about how you have to take the MT pcm to a dealer to get it reflashed with another car's VIN number. I'm planning on doing this swap, and am leaning towards buying a MT pcm as opposed to trying to figure out how to get my AT pcm re-engineered. What exactly would the process be? Upon receiving the mt pcm I would take it to a Ford dealership and ask them to do what?
 

cbxer55

Active Member
Jan 25, 2020
310
66
38
60
Oklahoma
I was thinking about doing this, when my auto failed me, TWICE. Sure glad I didn't. Sounds like PITA!
 

sosocrates

New Member
Aug 29, 2021
4
0
1
18
USA
Just finished my 5r55s to tr3650 swap in my 2005 mustang gt. Wanted to add a comment to this thread with some of the issues I ran into. I'm aware that this may make me look like an idiot, I prefer the word inexperienced. This comment will likely be of little use to anyone who already has automotive experience. I'm 18 and had no auto experience other than oil changes prior to the swap. I did not receive any help in real life. If you are mechanically minded, you can do it.

I went the route of modifying the auto wiring harness and getting the PCM tuned as opposed to replaced. I would recommend both. Modifying the wiring harness was not hard, and it is a lot cheaper to get the PCM tuned with a manual tune than it is to buy a new one.

One of the first issues I ran into was with rusty exhaust bolts; make sure you have some penetrating oil with you.

Please don't remove the transmission pan. I don't know why I thought I had to. Brainless moment I guess :confused:
I had planned to skip the transmission jack and just try to use normal jack stands and muscle to get the transmission out. Unless you have someone else who is willing to sacrifice their arms for you, please just get a transmission jack. Maybe you can bench press 100 pounds. That doesn't mean you can hold 100 pounds up with one hand while removing all the bellhousing bolts.

All the videos on how to remove transmissions on youtube were for manual transmissions, so I had no clue that I would need to unbolt the flex plate before I could remove the transmission. As a result, I spent around an hour wrestling with the transmission before giving up and going to bed. Try to avoid this lol. If you are still having a hard time getting the transmission out, you can jack up the front of the oil pan a little bit. This will rotate the engine a little bit, can help you get it out. Obviously be careful not to jack up the pully. I can't say for sure that this won't damage anything, but I've read about people doing it, and I had no issues doing it.

Wait to hook up the clutch fluid line until after you're ready to attach it to the transmission; I had brake fluid dripping on me for way too long. Also you might need more brake fluid, I had to top mine off.

If you're ever not sure about a wiring connection, you can use these quick splice connectors to check https://www.autozone.com/miscellane...e-blue-18-14-gauge-splice-terminal/310128_0_0

Soldering is not hard, don't let that scare you off. Also, it's like 10 dollars for a cheap one so they aren't expensive either.

When I was modifying the wiring harness, everything went well until I got to the neutral safety switch plug where you are supposed to solder the r/lb and w/p wires together. This is a plug with 12 wire connections, and 7 wires. One of those wires is white/pink, and another is grey/red. I was unable to find a diagram for that part of the harness until just recently, so I had no idea which one of those was actually the white/pink. (the red looked pinkish and the grey looked whiteish). I ended up connecting the red/blue wire to the grey/red wire :( with one of the quick splice things. When I tried to start the car, it obviously didn't start. I took of the quick splice and swapped the grey/red for the white/pink, and it still didn't start. It took me a long time to trace the problem to a blown fuse in the passenger side kick panel compartment area. I have wiring diagrams for the starting system and nss if anyone needs them. Just make sure you use the w/p wire not the g/r wire.

I had a bit of trouble getting the transmission back in. It just took me jacking up the front of the engine and raising up the bellhousing side of the transmission to get the input shaft to fit over the pressure plate fingers.

My car is currently giving me P0689. I'm not worried about this at the moment, I'll see if it goes away after a few hundred miles. I also did not hook up the clutch pedal position sensor so it is giving those codes as well.

In conclusion, I would not recommend this swap if your only reason is practicality. I personally wanted to do it because I wanted to learn more about cars, my auto transmission was on its way out, and I really love my car.

I got my transmission from Stan at pro-forceperformance.com. Took several months, but he was very helpful and his prices are great considering he sells reinforced and rebuilt transmissions.
I got the manual tune from Manuel at tudyno.com/index.html. He was also extremely helpful and definitely knows his stuff. I'm not sure I could have found the fuse issue without his help.

She's driving great, and I can't wait for the clutch break-in period to be up.