Yes my 04 gt had 2 piston calipers as well.
From research a large rotor (keeping pads and rotors same) would brake better. Something to do with torque, and larger rotor acts as better heatsink. Also saw something about smaller pad and the pistons on cobra are a little bigger, make more brake pad pressure, meaning more pounds per square inch.
So they will wear out faster but work better. So far so good, stop a lot better and no brake fade. Passenger side running about 100 or more degrees hotter. Going to bleed system again sometime this week.
It's a must to bleed the master cylinder when replacing calipers, I started with rear bleeder on caliper assuming it's for rear because you always start furthest from master.
Hope this helps anyone