If you're going to sn95 spindles then use the calipers from the car too. If you have the cash go ahead and buy some 13'' rotors and Mach/Bullitt/Cobra calipers. That is if you all ready have wheels that will clear the bigger brakes.
Any Mustang calipers from 94 to 04 will work, but the 99-04 base calipers are the best bang for the buck. They are aluminum, lighter, dual piston and look much better. The only reason to not use them is if you want to run skinnies in the front since some of them will not easily clear the calipers - the calipers are too wide with the brackets. You would need to grind a small bit for clearance on the spindles, but the newer calipers are much better than the older ones, and why not improve the braking while you are replacing parts?