The rotors will interchange no problem. assuming they are the 99-04 Brembo GT rotors and not the 13" Cobra rotors.
But the calipers are different. The 99-04 Mustang uses a dual-piston aluminum PBR caliper with greater clamping force than the 94-98 single piston steel caliper.
You can swap these calipers over you your car. You can score the 99-04 V6/GT calipers off ebay with lines for under $100.
Those calipers, along with the hawk pads and brembo rotors will swap to your car and give you a nice increase in braking performance. Remeber to get 99-04 brake lines too. you will need them