No, you can't fit 16" rims over Cobra brakes. (Your Cobra has 13 inch diameter front rotors. Stock GT and V6 94/95s have 10.8 inch front rotors.)
That's why lots of GT owners stick with the '99 and up dual-piston PBR brakes when upgrading the lousy stock front brakes on a 94/95 GT. They use the same 10.8 inch rotor, but a much better caliper.
If they go with Cobra brakes for the upgrade, and they have stock 16" waffle ponies on their GT, they'll have to buy a set of new wheels to fit over the Cobra brakes.