Well, if the system is 100% working right, then there is one thing you can try.
The 1993 Cobra MC is a 1" bore. The next size up is the 94-95 Mustang GT MC which is a 1 1/16" bore. Fortunately, the port sizes are the EXACT SAME as the 1993 Cobra, so is should be a direct plug and play without changing any of the lines. If it isn't, then the MC you installed was not a 1993 Cobra MC....however that's a long shot as I can't see Summit mixing it up.
Since this MC is regular production stuff, it should be cheaper, with even used versions in the $20 range as it's so common.
Now, ideally, the 1993 cobra should work fine, but since you are claming the pedal is soft, and travel is long, then you might want to try a larger bore MC as this will push more fluid. As a result, your pedal should firm up, and stroke should shorten.