maybe this will help some, but it may not be true for all brands of exhaust.
i have a 95 cobra with a magna pack cat back that is sold for 96-98 mustangs. at the time, when i bought it, magnaflow didn't make the magnapacks for 94-95 models. so i had bought the one for 96-98 and the only thing i had to do was slightly bend the passenger side pipe that goes from the muffler or what you would call a muffler, over the rear end and to the tail pipes. as it came from the factory it would sit too high and hit the bumper. it just need to be bent down very little, nothing that would distort the original shape of the pipe. the shop that installed it already knew this since they did another 94-95 with the same cat back. they also said it was common for the regular cat back from magna flow that is made for the 94-95 has had the same issue with the last part on the passenger side to sit too high.
and why would you trade a side exhaust with side skirt for a stock cat back and sideskirts, is something i will never understand. talk about getting the raw end of the deal.