I suggest a couple possible solutions:
First: Make sure that if you have a one way valve going to the brake booster from the intake manifold that it is working properly. A soft pedal can sometime be caused by the booster pressure being sucked back out by the intake vacuum.
Second: If it was a rear disc upgrade from rear drums than make sure the proportioning valve is the correct year match
Third: If you don't have brake cooling ducts (either trick or a simple hose) make them, try and direct as much air to the center of the rotor
Forth: You might be boiling the brake fluid (which creates steam albeit minute) but it is still air. Make sure you use Dot 4 or higher and don't use the bottle again once you open it. Once the seal is broken, the fluid will absorb moisture(some will contradict this but it is true).
Fifth: Replace brake system parts with the very best you can buy, there are cheap rotors available from parts stores that are poor quality, and if they get hot they warp, which will kick back the pads so each time you have to use the brakes you have to pump the pedal.
Sixth: Bleed the brakes every weekend, making sure that you don't have any air seep back in the system from the bleeder catch bottle etc.

Those are my suggestions, hope it helps.