Another thing to think about: even if the rotors are the same size (which I don't think they are), standard and premium GT rims have too much material on the inside of the rim spokes and will not clear the bigger brakes. You will need rims that clear the calipers as they turn. Rims with greater caliper clearance are part of the track pack. And make sure you have the right connecting/flexible brake lines that go from calipers to main brake lines.
The rotors are larger. You will have to deal with wheel clearance depending what wheels you currently have. Ford sells the upgrade as a kit, but it should be significantly cheaper to do using used or Rock Auto parts. When you bleed the brakes you may need to deal with the ABS computer activation, so plan for that.