Auto to Manual Trans ''How to'' guide

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.

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.

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?

I was thinking about doing this, when my auto failed me, TWICE. Sure glad I didn't. Sounds like PITA!

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
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.

Adding on to the last comment

Symptoms:
Very difficult/impossible to put the car in gear while running from a stop. Both first and reverse were like this. Went in fine while rolling, but from a stop I sometimes had to turn the car off, put it in gear, and start back up. Another get by that sometimes works is to put it in neutral, rev the engine a little bit, and quickly try to put it in gear. Doesn't always work though. This issue got worse the more I drove it.

Solution:
Add a shim or spacer to the throwout bearing. I had to drop the transmission back out, but it fixed the problem and didn't take too long having done it before. I am using the exedy mach 400 clutch kit as well as the exedy lightweight flywheel. I needed three spacers of width 0.156".
View: https://www.youtube.com/watch?v=o-rKpvfb_og


This video (if the link works) can help understand how much spacing you need. Before I added the spacers, I had a preload of 0.3" or so. After, I had around 0.8". I read somewhere on a different forum that some guy recommended a preload of around an inch for our cars. In the video, the guy says to go up to about 0.75". I am using a preload of around 0.8 and have had no issues yet. I was comfortable going over the preload the guy from RAM said because the ROM of the Exedy TOB is fairly large, and there was plenty of distance it still had to go as the PP got older. Also keep in mind that it will be fairly difficult to get the transmission back in after adding the shim. I needed longer bolts in order to get it in. I believe they were M10x1.25.

Just wanted to toss this in here as apparently its fairly common problem with the exedy clutch kit.

anthony05gt said:

There is a plug that used to connect to the transmission that has 12 wire locations on the plug. You will have to cut 2 wires at that plug and solder them together using heat shrink tubing. Cut the 2 wires colored red/light blue and white/pink and solder them together. This will allow the engine to start later. They are the only 2 wires on this plug that will be used. After you solder the wires together tape up the plug like you did with the other no longer used plugs or cut the plug off completely and tape up the wires. Again, you should probably use some rtv silicone to help seal off the wires along with the tape.

Click to expand...

Hi, I made an account here cause I've come across a little roadblock on my swap in my 2010.
On the big round 12 wire plug that inserts into the transmission and has rubber O-rings. You say cut and solder together the red/light blue and white/pink wires. Well my plug is 11 wires and doesn't have either the red/light blue wire or the white/pink wire.
The 11 wire colors if got are;
1 green/blue
1 green/white
1 blue/orange
1 purple/white
1 grey/yellow
These 5 are on 1 side of the plug
On the other side of the plug are these 6
1 blue/beige
1 green/white
1 grey/beige
1 grey/yellow
1 yellow/beige
1 green/beige
Do you know which 2 I need to cut and solder together?

Also the 3 auto harness connectors that connect to the top side of the auto, the rearmost one is the one I cut and solder on the new pigtail for the manual speed sensor Im guessing right? I say this cause all 3 plugs have the same color wires.

Side not, do you know where I can get a pigtail to plug into the tr3650 speed sensor? At my local ford they want like $80 for one. everything I find online is either for the older T5's or for T56/TrR6060's.

TheCrowdPlow said:

Hi, I made an account here cause I've come across a little roadblock on my swap in my 2010.
On the big round 12 wire plug that inserts into the transmission and has rubber O-rings. You say cut and solder together the red/light blue and white/pink wires. Well my plug is 11 wires and doesn't have either the red/light blue wire or the white/pink wire.
The 11 wire colors if got are;
1 green/blue
1 green/white
1 blue/orange
1 purple/white
1 grey/yellow
These 5 are on 1 side of the plug
On the other side of the plug are these 6
1 blue/beige
1 green/white
1 grey/beige
1 grey/yellow
1 yellow/beige
1 green/beige
Do you know which 2 I need to cut and solder together?

Also the 3 auto harness connectors that connect to the top side of the auto, the rearmost one is the one I cut and solder on the new pigtail for the manual speed sensor Im guessing right? I say this cause all 3 plugs have the same color wires.

Side not, do you know where I can get a pigtail to plug into the tr3650 speed sensor? At my local ford they want like $80 for one. everything I find online is either for the older T5's or for T56/TrR6060's.

Click to expand...

I believe you're looking at the wrong plug. You need to look at the plug that has 7 wires.

jayden2013 said:

I believe you're looking at the wrong plug. You need to look at the plug that has 7 wires.

Click to expand...

Yes you are correct, I got it all figured out though I think. Ive already soldered my 2 wires together although mine where different colors than the white/pink listed on the guide. Mine where green/orange and dark blue/white I believe. I havent tried starting my car yet but I will soon enough.

TheCrowdPlow said:

Yes you are correct, I got it all figured out though I think. Ive already soldered my 2 wires together although mine where different colors than the white/pink listed on the guide. Mine where green/orange and dark blue/white I believe. I havent tried starting my car yet but I will soon enough.

Click to expand...

Good to hear. And to answer your other question, dorman part number 645-213 works for the speed sensor. You might have already bought the pigtail but just for anyone else reading this thread in the future.

jayden2013 said:

Good to hear. And to answer your other question, dorman part number 645-213 works for the speed sensor. You might have already bought the pigtail but just for anyone else reading this thread in the future.

Click to expand...

Thats correct too. Another question, do you know the part number for the wiring harness to plug into the cruise deactivation switch and neutral safety switch on the clutch pedal? There is a unused plug up under the dash, but its a different connector.

TheCrowdPlow said:

Thats correct too. Another question, do you know the part number for the wiring harness to plug into the cruise deactivation switch and neutral safety switch on the clutch pedal? There is a unused plug up under the dash, but its a different connector.

Click to expand...

The only part number I have been able to find is 7r3t-12638-ab and it seems to be 07-09 specific. I jumped the wires on the neutral safety switch for the time being until I can find the wiring harness or decide to wire my own pigtails.

jayden2013 said:

The only part number I have been able to find is 7r3t-12638-ab and it seems to be 07-09 specific. I jumped the wires on the neutral safety switch for the time being until I can find the wiring harness or decide to wire my own pigtails.

Click to expand...

I was just at my local ford today and that part is discontinued. So my best bet is to go to a junkyard and find a wrecked one. Think V6's will have the same harness? I doubt there are many wrecked mustangs in my area, I'm pretty rural. Im not too concerned about the neutral safety switch working, I just really want my cruise to be functional. Know anyone or anywhere I can maybe find this wiring harness used?

TheCrowdPlow said:

I was just at my local ford today and that part is discontinued. So my best bet is to go to a junkyard and find a wrecked one. Think V6's will have the same harness? I doubt there are many wrecked mustangs in my area, I'm pretty rural. Im not too concerned about the neutral safety switch working, I just really want my cruise to be functional. Know anyone or anywhere I can maybe find this wiring harness used?

Click to expand...

The v6 and v8 should have the same harness. There's currently one for sale on ebay right now.

OK old thread I know but i just did this and have some questions. Everything is working BUT the reverse lights are doing their own thing. After rereading I realized that was mentioned at the beginning. BUT I am curious if you find and cut the wire at the Sill plate will the reverse lights just be totally inoperable and stay off? I may eventually do the wiring but right now just trying to get the car to work without the lights coming on when they want to.

Other thing I want to note. I got everything off a used car that i was taking the motor to replace mine anyways (bent a rod). Using auto harness that I modified (thanks to this post) and my old PCM. Weird thing is the cruise control works, but there is the part where it doesn't shut off when i push the clutch in because I have not put in the switch or harness. BUT it works lol.

I have done the swap using manual pcm as well as manual harness. I did not get the harness for neutral safety switch under dash so I read where I am was supposed to connect a grey/yellow and black wire that were going into a connector with a white wire as well above clutch pedal. So I connected grey/yellow and black and left white wire in connector. Still no crank when turning key, all lights come on but when I turn key to start nothing happens. Is there still going to be the connector with 12 plugs where I need to connect the w/p wire with the r/lb? I have noticed the plug that went into the auto shifter under cupholders, so far it’s just left unplugged. I would love to get it running so I can have it tuned. Any and all help is appreciated.

Dude I just wanted to say almost 20 years later you made this swap a breeze for me. Thank you so much dude.
Also btw you can use pigtails from a v6 5 speed as well. I just so happened to have one laying around.