Yes, those are cobra calipers.
That caliper was initially designed for 12" rotors and later adapted to 13", so you can see why it doesn't touch some of the rotor. But your setup is correct. Your rotor is an aftermarket rotor that has a tigher hat area that the OEM rotors, so it exaggerates how much area of the rotor faced is not being contacted. the OEM rotors give a slightly smaller area.
The 94-04 Mustang calipers are an interesting mix of fine and course banjo threads and m10 and 3/8 threaded bleeder ports. Ford changed things around for some reason.