Yeap, sure will. I have a 90 Cougar and I have a lot of parts off of various SCs. There are some minor differences in wiring, cant recall exaclty what, but I do remember swapping a computer into my 89 Cougar a long time ago from a 90 SC and it wouldnt charge for some reason. As far as wiring and as far as modules go, just compare pin to pin on the EVTM(wire drawings) and that will answer any other questions.
1994 Mk VIII in RCOH
1990 Cougar XR7 - ALIVE! 325RWHP at current tune
1981 Rabbit 1.6D + K03 50-60mpg