NO...the bell (and the trans is the same as a 95GT). No need to go changing any of that unless you want to swap it all over to foxbody length, which is 1" shorter. In 99 they eliminated the speedo gear hole, so you're screwed. 94-98 V6 T5s are perfectly useable.
The 4.6 "T5" is an entirely different animal. 4.6 specific bolt pattern, and they actually used the T45 and 3650.