Due to some complaints about pedal feel, Ford changed its M/C size to address those complaints. So the typical sn95 M/C size is 15/16" to 1-1/16" giving more firm to a more plush pedal assuming the same brake combo.
On my 86 GT, I was running the Cobra front brakes (I believe the 38mm PBRs) with 93 Cobra rears (45mm Varga with 10.25" rotor), and the 93 Cobra M/C with stock 86 booster. Pedal was very good - easy to modulate. Boost was more than enough. But I've upgraded to StopTech ST40s (4-piston) with 14" rotors, and swapped the rear to Cobra 38mm caliper and 11.675" rotors. According to StopTech, the ST40/14" is a perfect match for the Cobra rear. Given this I'm keeping the 93 Cobra M/C but moving up to the 93 Cobra booster because the stocker is done, and the motor is out making the install easier. Based upon my brake bias calculator, I expect the pedal to be about the same. Since the 00 Cobra Brembos are meant to work with the Cobra rear setup, I believe the 93 Cobra M/C should be OK. It's right in the middle and likely to provide great feed-back and modulation.
If you change the booster and/or M/C, be sure to get the brake rod length correct. See MM's M/C installation instructions for guidance.