94-95 will need to clearance the ears for the piston bores a bit. 96-98 will be direct bolt on.
Master Cylinder needs to be changed as well. That small tidbit gets overlooked. Yes, you can use the calipers with your original MC, but the design intent of the 99-04 GT/v6 calipers was to be used with a 1" bore MC when using a vacuum booster (ala the 99=04 V6 Mustang) The 94-98 GT/V6 uses a 1 1/16" bore MC, while the 99-04 V6 with vacuum brakes uses a 1" bore MC. The boosters are virtually the same.
So it's a 1/16" difference, but this is pretty big in terms of feel. The result will be with the larger bore MC, the pedal effort will be alittle harder. If you have strong legs and don't mind the effort, keep your original MC, but if you want a little easier modulation, a 1993 Cobra 1" bore MC would be a direct swap for your current MC. Just need to bench bleed it, install, and bleed the brakes.