Auto to Manual Trans ''How to'' guide

Discussion in '2005 - 2009 Specific Tech' started by anthony05gt, Apr 22, 2009.

  1. This manual was completely lost. I found my notes and re-wrote it with help from a couple of guys that had previously used it and saved important information. Read it very carefully before getting yourself into this swap.

    (1) 5r3z*7a512*a> tube (hydraulic hose)
    (1) 5r3z*2455*b> pedal assy (has master cylinder on it)
    (1) tremec 3650> transmission '05 up specific
    (1) f6zz*7007*ea> spacer plate (between engine,transmission)
    (1) 4r3z*7277*abd> gaiter (leather shift boot)
    (1) 4r3z*7a508*aa> slave cylinder (may come with purchased, used tranny)
    (1) ??????> rubber dust boot under the leather shift boot (Ford didn't have part #)
    (1) ??????> shifter (I bought an aftermarket used shifter that came with the bolt that
    mounts it to the transmission. Its a special bolt that you must have. You also
    need the linkage rod that connects shifter to transmission spool. The rod
    comes with the stock Ford junk shifter. The rod uses 2 plastic bushings that
    are also needed. I don't know if the bushings come with the linkage rod. If you
    buy an MGW aftermarket shifter it comes with the bushings (not the rod).
    (1) ??????> flywheel and 6 flywheel bolts (I used aftermarket)
    (1) ??????> pressure plate and bolts (6) I used aftermarket)
    (1) ??????> clutch disc (I used aftermarket)
    (1) f6zz*7600*a> sleeve (pilot bearing)
    (1) ??????> pcm (computer) Your computer can be reprogrammed to manual
    (1) 6r3z15520*aa> manual trans output shaft speed sensor (may come with used tranny)
    (1) xr3z*7h103*ab> reverse lamp switch (may come with used tranny)
    (5) ??????> top 5 bolts that hold transmission to engine must be replaced because they are
    shorter than what you had. The bolts cannot be cut and reused. Don't even
    try...get the new bolts.
    (1) ??????> shift knob (I used aftermarket)

    This swap can be done by modifying the auto wiring harness or by replacing the engine/tranny portion of the car's wiring harness. Both ways have their pros and cons. For example, replacing the section of harness is a pain and will take all day. Not replacing the harness and modifying the existing harness will require about a day and requires some soldering skills and will save you some money. You'll need to run a custom reverse light circuit that the car's computer will not see. I modified my existing harness and I'll show you how to do this later.

    The next part on the list is the last part you will need if you plan on replacing the harness section.

    (1) ??????> manual type engine/tranny portion of wiring harness (stick with the proper year)

    The next parts on the list are the extra things you will need to buy if you plan on reusing your existing wiring harness.

    (12 feet)> black wire harness convoluted tubing that's already all over your car's engine compartment.
    (2 feet)> heat shrink tubing for 16-18 gauge wire
    (1 roll)> black electrical tape
    (20)> medium size wire ties (zip ties)
    (1)> inline fuse holder with 10 amp fuse
    (1 roll)> multi stranded insulated copper 18 gauge wire (actually will need maybe 20
    feet of wire total)
    (1) 3u2z*14s411*vba> wire assy (pigtail) Ford part
    (1) 3u2z*14s411*sfa> wire assy (pigtail) Ford part (these 2 parts are the pigtail wire and plugs that
    will be soldered to your old harness and allow you to plug existing wires to your
    new transmission's reverse light switch and output shaft speed sensor)

    NOTE: You can get a shifter and transmission from They are almost sold out of the transmissions as of today (2-27-10) Ford will be switching to a new style tranny soon. The shifter comes with the needed linkage rod on this site and it's real cheap compared to your dealer. Also, the rubber dust boot under the shift boot can be obtained by people who have installed MGW shifters because the boot gets removed when using MGW. I think this is the absolute best shifter available so consider buying one...then you won't need the rubber boot and you'll really dig the way the shifter operates.

  2. its now a sticky :)
  3. gee, you would think this would create more chatter than this :shrug:
  4. Haha, thanks Bigcat. This is kind of a big jump for most people....but when they decide to do it the manual will help. Every once in a while (just recently) a flurry of people start looking for the manual.
  5. Finished

    I finished with my swap and everything went smoothly. I replaced the harness and PCM. I have not done the cruise control features. I'll add a version of my swap soon. A note to others; If you want to go with an after market shifter, most of them require reusing the parts of the stock manual shifter assembly. sells that for about 50.00 and it includes the rubber lower and upper leather boots

    My old parts are for sale on ebay sold together
  6. I have done so many 5-spd swaps here that i can do most if all parts are available in about 5-8hrs. But all have been fox on up to SN-95 cars, never any s-197's... but i imagine there isnt much more than the usuall right? PCM and re-cal, and all the driveline-pedals. Just curious because I know the day is coming when someone is gonna be like "dale can you do a s-197 swap?"
  7. My parts list has a note on the bottom of the page explaining the shifter details. When I got one from it only came with the shifter and linkage rod. That was for an '07 I did for a guy.

    Dalemllms, it's not complicated. Read over the link on the first post.
  8. Any of you guys live close to Cali...... Id be willing to pay in cash and beer if you could help !
    Steve McCracken likes this.
  9. Ha Second that on the willing to pay in cash and beer!

    Hey Anthony, I just went through both this forumn and the post in moddedmustangs, and the link for the manual seems to be either broken or no longer available. Just curious if it is still available. :p

    Also... For anyone who has done the auto to manual swap, realistically how much is it likely going to cost you "doing it yourself"? This has always been on the dream list since I first bought my V6, and unable to afford a gt at the time. :p


    This manual is for '05-'06 mustang gt swap. Newer cars require a slightly different approach.

    Remove auto transmission, flexplate, shifter (save all small nuts that hold shifter down, you'll need 2 for the manual shifter), front fascia, trans cooler, lines. MAKE NOTE AND MARK ALL FOUR 02 SENSOR WIRING HARNESS PLUG CONNECTORS. THEY CANNOT BE CONNECTED TO THE WRONG 02 SENSORS UPON REASSEMBLY. Remove brake pedal assy along with switches. Remove oval shaped foam rubber plug under dash on the firewall (driver's side) It's about 3-4 inches long. Remove shiny tape under the hood on the firewall that's in the same location that the rubber plug was (other side under hood).

    Install flywheel, pilot bearing, clutch package and engine/tranny spacer plate. Install transmission, driveshaft, shifter, shift linkage rod (with plastic bushings), rubber dust boot and leather shift boot. Install new dual pedal box assy. Connect the brake pedal linkage rod and twist the brake pedal switches back into their spots on the pedal assy. If you want a starter enabler switch on the clutch side of the pedal box, go to your dealer, get the switch and pigtail/plug and the wiring is there under the dash. Otherwise you will be able to start the car without stepping on the clutch. There's also another switch on the clutch side that shuts off cruise control. I didn't get that either and the cruise control DOES NOT work anyway since I did the swap. I don't know why and didn't research it because I do not use cruise control. now offers a swap kit...maybe they can shed some light on this subject if you want cruise control, but like I said, I didn't might.

    There is a hose under your hood now where the clutch master cylinder/pedal box was just installed. That hose gets connected to the side of your brake master cylinder reservoir on the nipple that's sticking out. You'll have to cut the end of the nipple off so brake fluid can flow out, then simply push the hose on and clamp it. Connect the hydraulic line that you purchased to the clutch master cylinder under the hood and run the line down to the driver's side of the transmission and connect that end to the steel tube on the side of the bell housing. The hydraulic tube just clicks on with a decent amount of pressure. Get a good look at another manual transmission car to see how to route the hydraulic tube down to the transmission. You don't want it to touch the steering shaft or get too close to exhaust components. Once the tube is attached and the reservoir (brake fluid) is topped off, the clutch will have to be bled. The easiest way to do that is to slowly pump the clutch pedal in and out very slowly for about 10 minutes. It should take you about 5 seconds to complete one stroke of the pedal. 5 seconds down and 5 seconds up. Do this for about 5 minutes and then go ahead and increase your pedal stroke speed to about 2-3 seconds per stroke for another 5 minutes. That will allow all air in the system to sneak out through the brake fluid reservoir.

    Before you installed the transmission you should have either replaced the engine/tranny portion of the wiring harness or decided how you are going to run the old auto harness in order to successfully connect all plugs to the new transmission and all four 02 sensors. Recently, a guy I helped through this swap did replace the engine/transmission portion of the wiring harness and still had to run a custom reverse light circuit. He was all done and the reverse lights had a mind of their own. We figured replacing the section of wiring harness would work, but it didn't. His pcm was reprogrammed for manual use, not replaced with a Ford supplied manual type pcm...maybe that has something to do with it. For this reason, I suggest you consider reusing your old harness. I'm sure there is an explanation for what happened in his case, but it's not my problem to figure out.

    This next section will explain what to do if reusing the old wiring harness. When I did the swap I also installed longtube headers which required me to extend 2 of the 02 sensor sections of the wiring harness. I chose to run my old auto trans wiring harness down the passenger's side of the transmission. I started with the 2 front 02 sensor plugs and just worked my way back. I connected the 2 front sensor plugs, snaked the harness back and connected the rear 02 sensor plugs. Remember to connect each 02 sensor to it's original wiring harness plug...don't mix them up. On the old transmission harness, tape up the large electrical plug that used to connect to the auto trans. Tape it up very well and neatly with electrical tape or just cut the plug completely off and tape up the ends of the wires. It's important to seal it well to keep water out. You may even want to use some rtv silicone sealant along with the tape to prevent any water from getting in. Do the same thing with the plug that has 2 wires colored dark green/white and gray/red. Do it again with the plug that has 2 wires colored gray/orange and gray/red. You won't be using these plugs again.

    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.

    There is a plug that used to connect to the rear of the automatic transmission with 2 wires colored dark blue/yellow and gray/red. Cut the wires clean right at the plug and get rid of the old plug. Solder the pigtail you purchased from Ford to the wires. Use the pigtail that has a plug on it that will fit the rear most sensor on the transmission. Make sure you verify the proper new pigtail plug of the 2 you purchased by connecting the plug the the rearmost sensor on the transmission for a test fit. You don't want to have to do it over again because of a mistake. Use heat shrink tubing to seal the soldered connection. After that, go ahead and connect the new plug/pigtail to the rearmost sensor on the transmission.

    This next section is where you will run a new, hand assembled 2 wire harness in order to have operating reverse lights on your car. To put it simply, your reverse lights already have a negative ground but will lack the positive voltage to turn on. You will simply be running a fused, positive wire to the reverse light switch and ultimately to the lights. When you put the transmission in reverse, the switch will connect the positive voltage and turn the lights on. For those of you who may shy away from electrical mods, relax. It's very simple so don't over think it and just follow the instructions.

    Take your roll of 18 gauge wire and cut 2 lengths that are long enough to reach from the car's under hood fuse box location, along the passenger's side valve cover, down behind the engine to below where they will end up on the driver's side of the transmission. One of the wires should be about 6 feet longer than the other and just left in the engine compartment hanging out of the protective tubing. The other wire should just be hanging out of the tubing maybe a foot or less at the fuse box area. What you should see is the black harness tubing from the fuse box area, along the passenger's side valve cover, behind the engine to the side of the transmission and at the fuse box area there should be one wire hanging out about 1 foot or less and the other wire hanging out about 6 feet. Secure the harness using a few wire ties (zip ties) along the valve cover. Down below, take the other pigtail/plug you purchased and solder it to the 2 wires you just ran down to the transmission. Use heat shrink tubing on the solder joint and connect the plug on the pigtail to the reverse light switch which is right in front of the rear sensor that you already completed work on. Don't worry about connecting the 2 wires anywhere on the other end yet (engine compartment). They will be connected later. Secure all of the wiring harness and plugs under the car with zip ties. Keep it all neat and don't allow any part of the harness to be pulled tight or near any exhaust components. I left all of the old taped up no longer used plugs up along the passenger's side of the transmission kind of high and out of the way. Just remember before you run any of the under car wiring at all to take the time to lay it all out an plan your route.

    Make notes and take your time to avoid hacking up your wiring harness. It's very easy work as long as you don't rush it. Also be sure your heat shrink tubing will be able to slip over your solder joints cleanly. I mean, if you wad up a lump of wire and solder the heat shrink tubing won't be able to slip over the joint. If you don't have soldering experience you might want to practice on some of the 18 gauge wire on the roll you bought. For those who don't know...heat shrink tubing is a protective insulation that is used on an electrical connection such as 2 wires soldered together. You simply slide the tubing on one of the wires before soldering, then slide the tubing over the soldered joint and use a cigarette lighter or heat gun to heat up and shrink the tubing tightly around the exposed joint. It also releases a small amount of heat activated glue which helps the seal become completely water tight.

    Remove the passenger's side inner fender well rear half. It's very easy and takes a couple of minutes. Once it's removed you will see where the main wiring harness goes through the firewall. On that rubber grommet where the harness goes through you will see an extra nipple that you can run your own wire through. Go back to the engine compartment and take the longer of the two wires in that harness you made and you will be running it through the passenger's side strut tower (hole is already there in the tower) along the sub frame and through the firewall. This should all be done through some of that black wiring harness tubing to protect the wire. Take some electrical tape and neatly tie the two harnesses together up in the engine compartment leaving the one extra (shorter) wire hanging near the fuse box. You will connect that later. There should be about 2-3 feet of wire and black tubing coming through the firewall into the passenger's side floor mat area. Use zip ties to keep the wires secure in the wheel well area away from suspension parts. Reinstall the inner fender well rear half.

    Pull the passenger side kick panel and sill plate. Open the wiring harness at the front area of the sill plate and find a white wire with a yellow stripe. Open the trunk and go to the right rear tail light wiring harness. There's more than one white/yellow wire at the sill plate so you have to probe the first one you find (I used a razor blade to sink into the wire and connected my meter lead to the blade.) Check for continuity between the white/yellow wire at sill plate and the white/yellow wire at right rear tail light fixture. If no continuity, find another white/yellow wire at sill plate area. Once you get the right wire with continuity cut it at the sill plate. Solder your wire that comes through the firewall to the rear half of the white/yellow wire you just cut. Tape off the front half. You want your wire to be soldered to the half that goes to the rear of the car. Use heat shrink tubing after soldering. Button up the sill plate and kick panel area, you're done there.

    Go to the rear of the car and carefully strip off some of the white/yellow wire's insulation, but don't cut the wire. You want to solder an 18 gauge piece of wire to the stripped area so that you are teeing into it. Run your wire through the rear steel body panel over to the driver's side tail light wiring. Clip the dark green wire with the orange stripe at the driver's side tail light fixture and tape off the part that goes to the vehicle's main wiring. Solder your wire that came from the passenger side to the half of the dark green/orange wire that goes directly to the tail light fixture. Use heat shrink tubing. Button up the trunk're done there.

    Go back to the engine compartment and take the other wire that comes up from the transmission switch and attach a 10 amp fuse to it, then from the fuse go to the rear of the fuse box and attach it directly to the heavy cable connection that's at the rear of the fuse box. The fuse will blow if any of your wiring should ever short out. Keep in mind...this connection is always hot, so don't leave the car in reverse when parked because the lights will stay on even with the key off. If you want to find a hot wire that's only hot when the key is on go right ahead....just plan your homemade harness according to that connection.

    The issue of the car's pcm (computer) is one important item you will have to deal with. I did this swap back in '05 and very little was known. As far as I know, I was the first guy to do this swap and I assumed I needed a manual transmission pcm so I bought a Ford remanufactered pcm. I later found out that on '05-'06 cars the pcm can be set up for manual type eliminating the need to purchase one.

    Any competent 3-valve tune professional can re-engineer your pcm to work for you. I still don't know for certain if it's best to buy a pcm and a manual type engine/transmission portion of the wiring harness both in order for the cruise control to work. I mean, I reused my auto harness and replaced the pcm and do not have cruise control anymore. Another guy I know replaced the harness, but re-engineered the existing pcm and he doesn't have cruise control either. Maybe someone else out there will be the one to shed light on this. Like I stated many times before...''I do not ever use cruise control and it's not my responsibility to figure it out for everyone else''. This information right here is free of charge to everyone and I'm glad to help people with similar interests as me.

    I do know that if you have your pcm re-engineered by a true professional it will be a simple plug and play deal with no issues...just start the car and go. If you replace the pcm rather than re-engineering it there's whole host of other things you'll have to deal with like a trip to the dealer where the tech will need to have a donor car for the set up of your new pcm and the parts guy will need a VIN# when you ask for the pcm. I had to find a similar equipped '05 car and use it's VIN#. I used Justin Burcham's VIN# because it was equipped just like mine, required the same smog control program and all except his car was a manual shift car. I think there are about 5 different pcms made for each year car depending on what area of the country you live in. For example, a California pcm is different than one for Maryland.

    If you have any questions about this manual just send me a PM. Please don't post any questions here because I don't plan on visiting this sticky all the time.
  12. Anthony, I acutally have your original site of the swap instructions backed up. I can email it to you in a zip file. Send me a pm.

    Im finally gonna do the swap seeing as my auto is starting to slip.
  13. The issue of the car's pcm (computer) is one important item you will have to deal with. I did this swap back in '05 and very little was known. As far as I know, I was the first guy to do this swap and I assumed I needed a manual transmission pcm so I bought a Ford remanufactered pcm. I later found out that on '05-'06 cars the pcm can be set up for manual type eliminating the need to purchase one.

    Link Building
  14. How much does it cost for this swap?
  15. +1 also curious. This is one of my dream mods besides a blower

    I'd imagine around $2,000 but if you could find a cheap tranny and sell your old one it might not be as bad
  16. if you're gonna go manual why not go 6spd?
  17. You can, but it's more money. Your auto and other parts are worth about $800 for the trans and a couple of hundred for the cooler, pedal box, shifter.

    You can do it for less than 2k if you do your homework.
  18. just did this swap (well had it done, i supplied the parts). i went the route of reprogramming the pcm, so far it's a headache. if you're thinkin about doin it, do so at ur own risk. if you know a tuner that's done the job before with no issues, i'd go for it, if it's their first time though, be prepared for a headache.
  19. Best bet is to have your existing PCM reprogrammed by a competent tuner. From what I've heard this can be done on all '05-'10 pcm's now.