i'm pretty sure they are....over at corral i found a couple threads saying that they are and they only thing not interchangeable between 96-98 cobras and gt's are the catbacks due to the different hangers. matter of fact, i'm planning on swapping a bbk catted x from a 98 cobra to my 96 gt on wednesday so i'll let you kno whats up after that.
actually, all 98 GTs and Cobras have the different style rear exhaust hangers (similar to the 99-04 style hangers)...94-97 GTs and Cobras use the same part number catbacks...
i thought it would fit on my 96 gt. it would have fit if the tranny was 5 speed instead of the huge 4r70w....the x pipe was off a 98 cobra and it rubbed against crossmember and there wasn't enuf clearance for the o2's. so all in all, the 98 cobra x pipe DID NOT fit my 96 gt due to the 4r70w.