First off, it will work without any problems. The hangers are in the same locations. It should just bolt right on. (trust me, I put a '97, '02, and an '03 GT catback on my '98 v6 when I had it)
Differences between 94-04 exhausts...the hangers:
From my experiences:
-ALL YEARS have the same muffler hangers, except 99+ have an extra hanger that hooks onto the side of the muffler that is closest to the outside of the car. You really don't need this additional hanger, I think it just keeps the mufflers more level/straight.
The big differences are in the tailpipe hangers:
-94-97 have a hanger on the exhaust tip that is perpendicular to the pipe.
-98-04 have the hanger on the tailpipe running parallel with the tip.
Other than the differences in the tailpipe hangers, any 94-04 catback will fit on any 94-04 GT. There is no differences in h-pipe connections/location, pipe placement, anything.
-ALL YEARS have the same muffler hangers, except 99+ have an extra hanger that hooks onto the side of the muffler that is closest to the outside of the car. You really don't need this additional hanger, I think it just keeps the mufflers more level/straight.