Wow! You just opened a can of worms, there! You'll get one of two replies from that question, in this forum. One) "Makes no difference/waste of time and money--go longtube!" Two) "Makes no difference, on an engine with your mods--go shorties!"
In short, (and without personal opinion) yes, they will work. As far as I know, the only difference between Fox and 94-95 GT headers is the port for the EGR.