1994 Aspire Brake System

You have the wrong master cylinder. Two different size bores is called a "step bore" and is used for "quick take-up" operation. That means the front calipers release more than normal, presumably for better fuel mileage, but then the brake pedal has to be pushed too far to the floor to reapply those calipers. The larger first piston moves a larger volume of fluid initially to get the front brakes applied so you don't have to push so far on the pedal.

Because you have the wrong master cylinder design, there are very likely other differences, and one of those could be the need for a different length push rod that is pushing on the primary piston. If your push rod is too long for this master cylinder, it will keep it partially applied and the lip seals will block the fluid return ports. That will prevent the brakes from releasing. As they drag, the fluid will heat up and expand. That applies the brakes harder and makes them heat up more.

A fast way to tell if the push rod length is the problem is to loosen the bolts holding the master cylinder. 1/8" should be plenty. If the brakes release, that is further proof you have the wrong master cylinder.