Who ever told you that it wouldn't fit didn't know what they were talking about. Some systems require the use of different hangers for 4.6 cars (for whatever reason) however, the system itself will bolt right up.
It will work. Only thing different is the hangers on the tips. 94-97 can use the same catbacks cause hangers are the same. while 98 has 99 - 04 style hangers. Any muffler shop could change that