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Auto to Manual Swap - 02-22-2008

0 - Introduction|

S197 Service Manuals: http://iihs.net/fsm/?dir=1
The service manuals above will be referenced in most of the removal sections for you to acquire a deeper understanding of what you're doing and how.
You should already be prepared with all socket sizes and wrenches.

Some rare tools and products you want to be prepared with:
1. Clutch alignment tool (you should be able to borrow one from Autozone, although the pilot bearing end of the tool may need to be sanded down to fit)
2. Torque wrench (you may also need a 1/2" to 3/8" socket convertor to fit your current socket set)
3. A pan for draining fluid
4. 3 quarts of new transmission fluid
5. A small funnel that will fit the fill hole of the manual transmission
6. Red loctite
7. Blue loctite
8. Anti-seize
9. A pry bar
10. A cheater bar (or breaker bar)
11. Inverse Torx socket set

The entire swap took me about a week of REAL work. A little over 2 weeks all together since I ran into trouble with the wiring harness and I was missing parts.
Plan to be without the car for at least a week.


0.5 - Parts List|

All of these parts must come from another MANUAL V6 car. A good bet is to find someone doing a V8 swap, as they need to get rid of nearly all of the following parts.

2005 and 2006 parts are interchangeable.
If, however, you swap wiring harnesses with a 2005 and 2006 car, connector C110 needs to be spliced in from the original harness. If you are not capable of soldering wires, purchase the wiring harness from a car that was manufactured the same year as yours.

I am not sure if 2007 parts are interchangeable. To be safe, if you own a 2007 car, purchase all of your parts from another 2007 car.

Flywheel with pilot bearing pressed into the center

T5 manual transmission

Slave cylinder with throwout bearing

Pressure plate and clutch disc

Rubber shift boot, not available from dealer

Hydraulic hose for the clutch

Leather shift boot (gaiter)

Dual pedal assembly

Shifter and shift ball


Engine wiring harness

Spacer plate

Starter motor


1 - Swap Pedal Assembly (206-06.Removal and Installation)|

Remove the aluminum tape on the driver's side firewall.
Remove the perforated foam to the left of the brake pedal.
Twist bottom sensor clockwise to disconnect.
Twist top sensor counter-clockwise to disconnect.
Remove plastic cover on pin.
Remove pin.
Remove 6 15mm bolts using a deep well socket and an extension.

Reverse removal process to install the dual pedal assembly.

2 - Remove Center Console (307-05.General Procedures)|

With the car off, shift the car into 1st and pull the e brake as far as you can.
Remove the trim black plastic trim around the base of the shifter.
Open the center console.
Remove all of your materials from within the console and in the cup holders.
Remove two screws at the rear of the console.
Remove the black cup holder assembly from the console.
Pull off (pull straight back) the plastic dash trim to the left and right of the stereo.
Remove two 10mm bolts from the bottom of the inside of the console.
Remove entire console.

3 - Jack Up The Car|

Put the car in park and pull the emergency brake.
Place chocks behind the rear wheels.

Lifting the front:
You may choose to use either the K member or the pinch welds (cut-outs behind the front tires underneath the rocker panels) for your jacking point(s).
Stop pumping when the car is high enough to fit jack stands under.
Place the jack stands on a solid part of the K member on each side of the car.
Lower the car onto the jack stands very slowly and carefully.
Make sure someone is watching the underside of the car to make sure everything sits correctly.

Lifting the rear:
You may choose to use either the flat part underneath the differential (although it is not reccommended in the service manual) or the pinch welds (cut outs in front of the rear tires underneath the rocker panels) for your jacking point(s).
Lift in the same fashion that you lifted the front.
Stop lifting when the axle is high enough to place jack stands under.
Place a jack stand on each side of the differential under the axle tubes.
Note: I did not lift the car all the way up the first time around because I wanted to be safe.
Note: I used 3 ton Craftsman jack stands that went up to 21" ($20 at Sears) - I had them on the 6th notch.
Note: I also added ramps and wood to strategic locations just in case a freak accident should occur.

4 - Remove Exhaust (309-00.Removal and Installation)|

Disconnect 2 oxygen sensors from both catalytic converters.
Remove the 2 bolts on each catalytic converter with a 12mm socket and/or 12mm flex head ratchet wrench.
Depending on your exhaust setup, the removal process will vary.
Set the exhaust aside.

5 - Remove Driveshaft (205-01.Removal and Installation)|

Remove the 4 bolts on each pinion flange pilot with a 14mm socket
Set the driveshaft aside.
Note: Some type of breaker/cheater bar will be needed, such as a pipe.
Note: The driveshaft flanges fit on the pinion flanges very tightly, and a pry bar will be needed to lift a driveshaft flange off of a pinion flange (It was either a nail claw or a cat's paw that worked for me).
Note: You can use the e-brake and/or the transmission park to lock and unlock the driveline for removing the driveshaft bolts and rotating the driveshaft.

6 - Drain Automatic Transmission Fluid (307-01.General Procedures)|

Remove the large drain plug on the bottom of the transmission pan and let the fluid drain into a large bucket or pan.

7 - Support the Transmission|

Place a thick and decent sized piece of wood on top of a hydraulic floor jack and align it, somewhat centered, under the transmission pan.
Pump the jack up just enough to place pressure on the transmission and possibly lift it up a mm or two.

8 - Remove the Crossmember (307-01.Removal)|

Remove the four outer bolts on the crossmember with a 19mm socket.
Remove the center bolt with a 13mm socket.
Set the crossmember aside.

9 - Disconnect the Shifter (307-01.Removal)|

Disconnect the shifter cable from the lever (you can pry the cable off of the ball joint, don't worry).
Remove the outer side bolt on the metal bracket with a 10mm wrench.
Remove the bottom bolt on the metal bracket with an 8mm wrench.

10 - Remove the Starter Motor (307-01.Removal)|

Remove the two bolts holding the starter motor onto the transmission with a 10mm wrench.
Either place the starter motor in a position that takes tension off of the starter motor cables, or hang the starter motor from the driver's side header with wire.

11 - Remove the Torque Converter Nuts (307-01.Removal)|

Look through the hole in the trans where the starter motor used to be.
Push upwards on a gear tooth with either a long screwdriver or a pry bar until a nut is easily accessible.
Remove the nut with a 15mm deep well socket as well as a breaker/cheater bar (The plate will spin when you try to remove a nut, but the socket will collide with the engine and stop the plate from spinning).
Repeat until 4 nuts are removed.
Note: The transmission must be in neutral for you to be able to spin the driveline to access the nuts!

12 - Lower the Rear of the Transmission (307-01.Removal)|

Remove the two lower retaining bolts on the transmission bellhousing with a 14mm socket or wrench.
Release the pressure in the hydraulic jack very slowly and let the rear of the transmission drop 6 inches or so, just enough to get access to the sensors and the upper retaining bolts on the bellhousing.

13 - Remove the Transmission Connections (307-01.Removal)|

Unscrew the outer nuts on the transmission cooler lines with a 19mm open ended wrench.
Note: Fluid will probably be pouring from the cooler lines, so place a pan underneath the cooler lines to collect it.
Undo the hose clamps on the transmission cooler lines to the rubber hoses from the transmission cooler. Remove anything else holding the transmission cooler lines in place and yank the lines out of the rubber hoses (this will take a lot of force).
Note: You have no use for these lines anymore, and nothing will be replacing them.
Disconnect the large rectangular sensor on the side of the transmission (transmission range sensor).
Disconnect the three square sensors along the top of the transmission (turbine shaft speed, output shaft speed, intermediate shaft speed), you will need to push down on the top of them and pull (I used a screwdriver to push down on the top of the clips).
Pry the two or three metal harness retainers off the metal nipples on the transmission.
On the last sensor, in front of the transmission range sensor, there is a bolt going through from the top; remove this with a 10mm wrench.
Once again, pry the second shifter cable off of the ball joint.
Note: The service manual says to disconnect the transmission cooler bracket from the engine (I didn't and the tubes did not get in the way).

14 - Remove the Automatic Transmission (307-01.Removal)|

Remove the top retaining bolts from the bellhousing with a 14mm socket or wrench.
Remove the side-top retaining bolts from the bellhousing with a 14mm socket or wrench.
Jack the rear of the transmission back up so that it is level.
Remove the side retaining bolts from the bellhousing with a 14mm socket or wrench while someone is holding the rear of the transmission to stabilize it.
Pull the transmission back away from the engine and begin to lower it (make sure at least one person is stabilizing the transmission on the jack the entire time).
Once the jack is lowered all the way, gently roll the transmission off of the jack and pull it out from under the car.

15 - Swap the Wiring Harness|

Unplug the top and bottom connectors on the PCM and work your way back from there unplugging all of the other connections on the automatic wiring harness.
Once everything was unplugged, I pulled the wiring harness out through the back of the engine down by where the transmission used to be.
Note: There are many plastic pieces holding the harness in, if you break them it's no big deal.
Note: There is one 14mm bolt holding the wiring harness to the back of the engine block at the top.
Feed the new harness through the appropriate locations and make the proper connections.

16 - Remove the Flex Plate|

Lower the hydraulic jack that is supporting the engine and remove it.
Stick a screwdriver through one of the holes on the flex plate that is over the hole where the starter motor goes.
Hold the screwdriver there and use it to stop the flex plate from rotating as you remove the bolts.
Remove the bolts with an inverse Torx socket and a breaker/cheater bar.
Steady the flex plate as you remove the last bolt, both the flex plate and a small spacer will fall down.

17 - Install the Flywheel|

Hold the flywheel up to the rear of the engine with one hand and hand tighten all of the flywheel bolts.
Remove one bolt at a time and clean it with brake cleaner, then cover the threads in red loc tite and put it back into the flywheel.
Once all bolts are back into the flywheel, tighten them in a criss cross pattern but not up to full torque.
Once all bolts are tightened, torque them in a criss cross pattern to 70 lb-ft.
Note: Clean the flywheel friction area with brake cleaner!

18 - Install the Pressure Plate|

Stick a clutch alignment tool through the center of the clutch, with the 'Engine Side' facing away from you.
Insert the end of the tool into the center of the flywheel (the pilot bearing).
Note: Before the next step, clean the pressure plate friction area with brake cleaner!
Place the pressure plate over the clutch and push it onto the flywheel's alignment pins.
Hand tighten all of the pressure plate bolts, and tighten them the same way you did the flywheel (along with the red loctite), only this time tighten to 26 lb-ft.

19 - Install the Clutch Hydraulic Hose|

Route the hose from the top left of the transmission area to the bottom of the clutch pedal in the engine bay (the 90 degree end will be in the transmission).
Attatch the straight end to the connector on the bottom of the clutch pedal in the engine bay.
Note: My hydraulic hose came with a connector already on it, and so did the transmission. I chose to take the connector off that was already on the hose.

20 - Fill the Transmission with Fluid (308-03A.General Procedures)|

Remove the drain plug, clean it, and apply blue loctite before tightening it to 13 lb-ft (just in case the previous owner did not do this).
Remove the fill plug (upper bolt).
Pump 2.8 quarts of automatic transmission fluid into the transmission.
Perform the same cleaning, prepping, and tightening procedure on the fill plug as you did on the drain plug.

21 - Install the Transmission|

Push the transmission up against the engine however possible, whether it be a lift or brute strength or what have you.
Make sure the transmission is flush with the engine/spacer plate before you begin to tighten the bolts in.
Support the rear of the transmission with wood or a jack.
Tighten the bellhousing retaining bolts.
Remove one bolt at a time, clean it, and put anti-seize on it, then tighten it back up.
Once all the bolts are clean, anti-seize'd, and relatively secure, torque them to 33 lb-ft, or however tight you can get them with a small socket wrench.

22 - Connect the Transmission|

Connect the two sensors.
Connect the hydraulic line.
Cut off the plastic end on the brake fluid reservoir and connect the tube from the top of the clutch pedal in the engine bay.
You will find a metal ring on the tube, slide this up to secure the tube on the brake fluid reservoir.
Sit in the car and slowly push the clutch pedal down and up, take 5-15 seconds per stroke (up or down), and do about 100 or so up and down strokes.
Note: This is a relatively easy way to bleed the line.
Note: You should start feeling pressure after a few strokes.
Note: Make sure no fluid leaks out of the bellhousing, that is a sign of a bad slave cylinder or a bad connection to the slave cylinder (if you have leaks, you may have to take the transmission off).

23 - Replace the Starter Motor|

Clean the starter motor bolts and coat them in anti-seize.
The top and side nuts on the starter motor need to be removed in order to put the wiring on the new starter motor.
Put the wiring on the new starter motor and tighten the nuts.
Place the starter motor inside its hole in the bellhousing, put the bolts in, and tighten them.

24 - Install the Crossmember|

Jack the middle/rear of the transmission up so that it is parallel to the ground.
Note: If you feel like it, you can coat the crossmember bolts with blue loctite, but it is not necessary.
Align the crossmember and tighten the middle bolt to the transmission.
Hand tighten the four outer bolts and then torque them to 46 lb-ft.

25 - Install the Shifter|

Where the old shifter was are two bolts coming through the floor under the car; clean these and put blue loctite on them.
Grease the shift linkage a little bit.
Align the shift linkage and the rear holes on the shifter and tighten the bolts/nuts to 30 lb-ft.

26 - Install the Driveshaft|

Clean all driveshaft bolts and coat them with red loctite.
With the emergency brake on, align the driveshaft with the rear flange on the differential and tighten the bolts to 76 ft-lb in a similar fashion that you took them off with.
Do the same to the front flange on the transmission.

27 - Install the Exhaust|

Clean the header bolts and coat them with anti-seize.
Align the exhaust with the header bolts and crossmember hangers.
Tighten the two header nuts on both catalytic converters to 33 lb-ft.
Connect the two oxygen sensors on both catalytic converters.

28 - You're Done|

Lower the car.
Make an appointment with a Ford dealership to get your manual PCM flashed to work with your keys (yes, I said KEYS, you need both of them).
When you get to the dealer, flash your current PCM back to stock with a tuner.
Hand the service person your new PCM along with your keys.
When you get your car back, drive home nicely.
When you get home, check the strategy code of the PCM and notify the person who created your tune. Have them send you a new MANUAL tune for the PCM.

Congratulations! If you need any help, you are welcome to comment.

2005 mineral grey aut...manual V6 | Demolet CAI | XCal2 VMP 93 tune | MAC long tubes | MAC O/R pipes | Pypes X pipe | Pypes high flow cats | GT take-off mufflers | 4.10:1 FRPP gears | FRPP T-Lok |
Auto->Manual Transmission Swap Tutorial

Last edited by temugen; 01-09-2011 at 10:06 PM.
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Good write up, I wonder how many more people will try this....

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nice guide brad, this will come in handy this summer

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Nice job The link to the S197 Service Manuals: http://iihs.net/fsm/?dir=1 alone is priceless!! Thanks

Mods/Upgrades: 1 of 8,519 GT/CS built in 2007 - professional tint, Factory plenum cover, MRT hood struts, MRT retro shift knob, SHR honeycomb rear black out panel, WebElectric Sequential Turn Signals, factory T-Lok with 3.55 gears, Shorty Antenna, Pypes Street-Pro mufflers w/ 4" polished stainless tips, C&L 95mm Racer CAI, custom SCT XCal II 87/93 HP Dyno Tunes, Black Powder coated twin beam strut tower bar, MRT Rear Window Louvers, Ford Bullitt grille and self designed one-off custom lower grille fogs, G-TechPro RR.

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So from a performance standpoint did you gain much. I was told by a guy with a GT mustang that the 5 speed auto's are so much quicker in the quarter mile. What is your experience. I would think that the manual should be say .25 to .5 seconds quicker same for same, tune hop parts etc. I myself have an 08 with V6 and 5 speed manual. So far car has gone bone stock 15.75 at 87.8 mph with two larger guys in the car and me bogging in first. Since then I have added a cold air kit Airraid, short shifter hurst, magna flow axle back exhaust, diablosport tune 87 performance octane tuneup, bbk 70mm throttle body, and other things like trim pieces sequencing tail lights and such. Have not run the car again on my g timer but car feels way quicker.
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The car definitely pulls harder now compared to the auto, but there's no way I could ever shift as fast as the auto did. Thus, the auto would win in the 1/4, but overall the manual is oh so much better.

2005 mineral grey aut...manual V6 | Demolet CAI | XCal2 VMP 93 tune | MAC long tubes | MAC O/R pipes | Pypes X pipe | Pypes high flow cats | GT take-off mufflers | 4.10:1 FRPP gears | FRPP T-Lok |
Auto->Manual Transmission Swap Tutorial
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What did this end up costing you overall?
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Originally Posted by LostGeographer
What did this end up costing you overall?
Trans, clutch, flywheel, driveshaft: $300
Shifter, PCM, wiring harness: $50
Rubber shift boot: Free
Dual pedal assembly, shift gaiter, hydraulic hose: $250
Total: $600

If you're going to do the swap, you might want to think about going directly to a 3650 or T56 with Nice Pony's adapter plate. That way you won't have to worry about the T5. I haven't had any problems with the T5 yet - it's solid and seems pretty well built (so far), but I know that it's not even considered a decent transmission.

2005 mineral grey aut...manual V6 | Demolet CAI | XCal2 VMP 93 tune | MAC long tubes | MAC O/R pipes | Pypes X pipe | Pypes high flow cats | GT take-off mufflers | 4.10:1 FRPP gears | FRPP T-Lok |
Auto->Manual Transmission Swap Tutorial
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wow where did you get your part's from do tell.

2005 SOHC Automatic V6 Ford Mustang

K&N aircharger Performance Kit
Single Flowmater A/T Exhaust
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I would also really like to know where you got your parts from if it wasn't just from a local junk yard.

2007 Mustang 4.0 v6 alloy, Automatic, CORSA mufflers with H-pype, SCT x-cal2, saleen suspension kit.
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