ssms has details on the swap
an xcal2 or sniper should be able to do it but you will need a to readjust the car tunes because the tunes sent were for auto originally
the harness ford is probably the only place or, junkyard
reason for that is because for manuals we have a clutch/saftey switch that will not let the car start with out the clutch pressed in from the car.
also a clutch cable will be need idk if i had said that before
heres the DIRECT copy from SSMS that'll cover everything you need and more:
AODE to T-5 Transmision Swap
1. What parts are needed?
Heres the list: 3.8 rear main seal, 3.8 pilot bearing, 3.8 dust shield, 3.8 flywheel, 3.8 bellhousing w/ballstud, 11”
clutch assy, 3.8 clutch arm, 3.8 T-5 transmission, speed sensor with speedometer gear, adjustable clutch cable, billet
clutch quadrant, clutch pedal assy, 3.8 T-5 specific computer (same model year preferred), 3.8 T-5 transmission
wiring harness, shifter, shift knob, weather shield (lower boot), shifter boot, various fasteners.
2. Do I need a T-5 computer? Yes, the computer must be swapped too. Source a computer, preferably from the
same model year.
3. How hard is it? The swap is pretty straight forward but its much easier using a lift. The hardest part is the swap
of the pedal assemblies.
4. What clutch options are there? You can use a direct replacement clutch available from Ford, or slightly better
replacement units from SPEC, RAM and others. For real performance or racing applications, the Ford stock
clutches usually prove to be inadequate. The 89-93 SuperCoupe clutch is much better, but its hydraulically released
and has other associated issues which require special shoulder bolts. The new Cobra 11 inch upgrade clutch
can be adapted to the 3.8 with some welding and grinding. However, SPEC has the best solution in its offerings of
four different clutches for varying horsepower ranges from mild to really wild (over 400 horsepower). We like
Stage 2 and 3 for most hopped up applications.
5. What flywheel options are there? We now have a race-quality SFI approved light-weight billet aluminum 11”
flywheel available that reduces the mass from 31 pounds to just 13 pounds for much quicker engine acceleration.
6. What would something like this cost? Estimate around $1200 or more for parts depending on availability. Labor
around $350-$500.
7. Why swap? For performance driving, theres no doubt that the manual is much more enjoyable. The manual
also minimizes parasitic losses in the drivetrain. For real performance, the auto needs improvements such as a
valve body type shift kit and a high stall converter matched to the output of the engine. Figure material and installation
for both at around $1100. However, if your auto has high miles and/or requires major service, the cost may
be a wash.
8. Can I modify the stock torque converter of my automatic to provide higher stall? We strongly recommend
against
modification of the stock converter. Why? That’s precisely the reason we swapped our AODE to the T-5.
The Art Carr modified high stall torque converter failed catastrophically which caused very small metallic particles
to pass into the AODE, subsequently trashing it and resulting in an $800 minimum AODE repair estimate. At this
point, an $800 repair and the cost of a high stall replacement converter ($800 or so) would be as high or higher
than the T-5 swap. In other words, a no brainer…in favor of the T-5.