Will a 2.5" pipe bolt up without problem or will I get a leak? If it is 2.25", where can I find an X-pipe that would fit, even MAC's site only has 2.5 now.
The stock exhaust is 2 1/4". Mustang Tuning sells a complete 2 1/4" midpipe (catted or O/R) now for the 96-04 V6 that will work with a GT takeoff catback: http://mustangtuning.com/exforv6mu.html
I personally would stay with a 2 1/4" exhaust to keep your bottom end torque intact.