Here I found this as well while searching for you:
Found Here:
http://modularfords.com/forums/f5/t56-swap-50493.html
96-98 Cobra T45 to 03 Cobra T56 Swap
The bellhousings on all modular mustang motors are the same so everything bolts up with no problems, including the starter.
In order to make the electric speedometer work in a 96-98 a speedcal extended range is needed.
http://www.dallasmustang.com/index.mvc?Session_ID=ba95e430b58caa8f3848ce694a652 50a&p=9910ER
The stock driveshaft will be too long so it will have to be shortened approximately 1 ¼â€Â. If you have the stocker shortened you will have to buy a slip yoke to fit the 03 cobra output shaft.
You can also buy a 03 cobra aluminum driveshaft. You will have to use the rear yoke off the stock driveshaft. The driveshafts are different sizes so a special u joint is needed. Precision u-joint part #448 fit perfect.
http://store.summitracing.com/default.asp?target=esearch.asp&N=100&Ntk=PartSearc h&Ntt=pcn-448&x=13&y=7
Reverse lights are the same between the trannies, no switching required.
The stock t45 crossmember and tranny mount bolt up the t56 with no problems. The crossmember will need to be moved forward. Move the rear crossmember bolt hole up even with the front hole on the framerail. Drill a new hole where the other hole in the crossmember hits the framerail. Do not use the exhaust hanger plate with the t56. The exhaust will be fine without it.
The tranny tunnel will need to be expanded in order for the t56 to fit without hitting. Use and hammer and expand it slightly along the passenger side and in front of the shifter. Do this BEFORE you install the tranny.
Clutch, clutch fork and throwout bearing can all be reused from the t45. Use the pivot ball stud that comes with the t56.
T56’s are equipped with a reverse lockout solenoid. This prevents you from shifting into reverse when downshifting from 6th to 5th. D&D sells the harness to make this work or you can buy a two wire pigtail connector. Run this to a switch or to the brake pedal switch. When you flip the switch or hit the brakes the solenoid will disengage, allowing you to easily shift into reverse. You can also leave the solenoid unconnected. It will require a little more muscle to shift into reverse but its not bad.
Leave the black tube that runs up the bellhousing alone. This is the vent for the tranny.
For fluid you can use dexron III or a synthetic fluid. GM syncromesh is supposed to make the tranny much smoother. Adding 2 oz. of ford friction modifier works well also.
http://www.steeda.com/store/-catalog/synchromesh.htm
The wiring harness for the t45 is plenty long enough to reach all connections on the t56. Run the wires over the tranny and not under.