Sure it will work

You need to have the shop install new flanges and change the angle to fit the V6.
I used a 94/95 GT BBK O/R X-pipe and had the shop modify it for me for $70 dollars total.
Here it is in action without mufflers.
www.youtube.com/crainracing
Sound quality is horrible because it was taken with a digi cam.
Thats a 96' Mustang with a 2000 splitport engine swap, ported heads and intakes and a few other goodies.