Originally Posted by bigdog99
If you only adjusted the pedal stop downward and didn't re-adjust the master-cylinder actuator rod (probably longer), then you created a full-time braking situation (which would lead to the result you have). As much custom work as you have done, I would be surprised if you missed this though...
The moment I read about your problem I also thought of this. There must always be a bit of free play on the actuator rod, if not the mastercylinder piston cannot move fully back to the rest position where it opens a small hole in the mastercylinder bore to allow the returning brake fluid back into the reservior. So every time you used the brake it built up more pressure in the system.