Complete Auto To Manual swap 2005-2009 Mustang Gt

Discussion in 'DIY Tech Guides' started by jbido, Mar 1, 2015.

  1. jbido

    jbido forum member

    Found this online. I thought someone might need it. I'm also doing this as soon as I get the parts.

    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.

    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.
  2. RetroGT2006

    RetroGT2006 06 S197 Member

    yup, I looked through that last year when I did mine.. The swap is so easy.. I have a thread on here about mine.
  3. 69Mach1-409

    69Mach1-409 Senior Member

    Not sure where you are located, but I have my takeout trans, driveshaft, flywheel, cross member, trans mount, and shifter. Might have some other pieces, but I'll have to check. They are out of a 2008 GT, have under 30k on them, and the DS has less than 5k on it.
  4. jbido

    jbido forum member

    @69Mach1-409 I'm in Essex county. I got the parts from the guy parting out the Roush. Is the driveshaft aftermarket?

    @Retrogt2006 I would love to talk to you I'm gonna be doing the swap soon and I'm a bit nervous. Your feedback would help greatly.
  5. 69Mach1-409

    69Mach1-409 Senior Member

    No, sold the aftermarket one awhile ago. I only have the stock one left.
  6. Aesthetics28

    Aesthetics28 forum member

    is this as simple with the 11-14's? my friend has an auto he wants to convert
  7. GreenTerror

    GreenTerror forum member

    As far as I know no one has ever figured out how to keep cruise control when doing this swap.
  8. GreenTerror

    GreenTerror forum member

    Bumping an old thread, would love to manual swap my car. Has anyone ever figured out how to keep cruise control working?
  9. JeremyH

    JeremyH 3V Fuel Guru S197 Team Member

    Requires man pcm or tuning and the correct harness.
  10. GreenTerror

    GreenTerror forum member

    Have you done this with your car? You swapped over the harness, or know someone that did it?
  11. JeremyH

    JeremyH 3V Fuel Guru S197 Team Member

    My personal car has always been manual. Those are just the things that are physically different auto to man wise that would effect computer controlled cruise control. The harness/sensors and pcm strategy/tuning, the man also uses inputs from clutch position sensor.

    Swap is not that uncommon some searching will come up with dozens of threads across multiple forums.

    If I was going to do it I would pick up a wrecked manual donor car personally.
  12. GreenTerror

    GreenTerror forum member

    Thanks, I've read many threads on the topic but I haven't been able to find one conclusion that showed they got cruise working. I always thought it weird because like you said there is only so much that is different between them.