Brakes 88 mustang brakes??

Which booster are you running? Should have the 93 Cobra booster with that combo as well

There's no reason to change calipers. That brake setup has been done a million times before with good results. It's basically a factory 1993 Cobra setup minus the booster. The 1" bore MC is ideal for the 60mm calipers, and 45mm cobra rear calipers. The setup us typically run with the 205mm booster, and not the stock fox booster, however many guys still run it with the stock booster with success.

WHat I would be checking is is there is a mechanical issue with the brakes. Do all the caliper pistons move freely? Are all the slide pins free? Perform some hard stops and use a cheap Harbor freight infrared thermometer to check the rotor temps and see if one is cold (one frozen piston will create a hard pedal condition). How do the rotors look? Do they all look the same in terms of condition, or does one look a little different with some score marks or heat spots? Rebleed all 4 brakes and make sure fluid flow is approximately equal and flows freely. I'd do all this before firing the parts cannon at it.

The 73mm calipers are almost 50% larger in terms of piston surface area than the 60mm units. When it comes to brake systems, that's huge without changing the MC and will result in a softer pedal, and longer stroke.

A better solution, if you don't want to change the booster, is the 94-95 cobra 15/16" MC which is about 15% less surface area than the 1" bore MC which will soften the pedal slightly and provide a slightly longer stroke. However, i'd check the entire system over thoroughly first.