there's IRS (independent rear suspension) rears, only used in cobra's for a few years, I think like 99-04, not really sure exactly. Then the most common is the solid axel 8.8s, used in mustang LX's GT's and cobra's. All the 8.8s are pretty similar, lots of parts will work is any stangs built in the last 20 or even 30 years.
HAHA, No they won't. Not much 99-04 drivetrain will work with a fox. MII's and previous cars have leafsprung rears. A 99-04 8.8 is almost as wide as a Panthers. IIRC wider than a T-birds. 79-81 Cobras didn't ave 8.8's. Older cars like 1st gens used bigger beefer axles like 9inches anyway. BUt yess 99-04 Cobras ae the only Cobras to have IRS. It's also heavier.
i think that the center sections of any 8.8 including IRS are all the same, gears, bearings and diff. axle splines are different tho, there is also a difference in axle size between a 99-01 cobra vs a 03-04 cobra. When you refer to cobra do you mean an IRS set up or older fox body? because im 99 percent sure the only difference between a cobra and regualar gt in the fox bodys and 94-98's was 4 lug and 5 lug? dont quote me on it there are more people on here smarter then me but thats what i have seen.