Pinion flange is different, yes both cars have t45's that is correct however the pinion flange is in the back of the car. So you'll have to swap driveshafts also
Edit for ref here is the part number for a frpp alum driveshaft
Specifications:
- Ford Part# M-4602-J
- Fits 1996-04 Mustang with manual transmission
- Fits 1996-98 Cobra 4.6L with manual transmission
- Fits 2003-2004 Mach1 with manual transmission
- 31 spline yoke
- High strength, 3.5" diameter 0.114" wall thickness 6061-RT62 aluminum seamless drawn tube
- 1330 U-joints 45.5" long (CL to CL of U-joints)
- Will not fit 1999-04 Cobra