Have you considered Wilwood brakes? They make a variety of brake kits with single or multiple piston calipers?
This is one of their kits for 87-93 Mustang - 12.2" with 4-piston calipers (requires 16" wheels though):
Or, like I'm going with, 13" with 6-piston calipers (front)(requires 17"+ wheels):
There is also BAER, an EXCELLENT choice with options up to 15" rotors ($$$), or SSBC. All excellent brakes for the Cobra