Only if you get a solid rear that does not have ABS. The TCS works off the ABS wheel sensors.
I beleive all Cobra's have ABS, but not all GT's.
Keep in mind any 94-98 rear end will be narrower than the 99=04 rears. About 1" each side. If you use a 94-98 rear your real wheels might look sucked in.
You could add the ABS to a GT rear without it, but you would need the sensors and the ABS wheel hubs. The hubs i beleive are pressed onto the axles. It's kinda a pain in the ass to do. Make life easy on yourself and just trade rears with a guy with ABS already.