Sounds like your brake pedal rod is to long and applying to much pressure on the system at all times thus heating up the brakes. If your master was not bench blead it needs to be and that is a seperate issue.
It sounds like you may have multiple issues happening at once. As Todd stated, if your push rod is too long, it may not be allowing the piston in the master cylinder to fully retract. This can cause the pressure at the calipers to not release and the lock-up scenario you described. A quick and dirty way to check it is to open a bleed valve on a caliper and see if that unlocks the caliper with a squirt of fluid.
Your pedal feel would certainly suffer if the system has not been fully bleed of air. It's also possible that your MC is not properly sized for your disc/disc combination or that the MC is not compatible with your setup.
Update: The mc was bench bled. I tracked down the manufacturing tech support guys and basically there are 2 holes on the brake pedal bracket that the rod attaches to. My friend hooked it up to the top one, which is where the old manual brake rod was attached to. The bottom one is apparently for power assist brakes. So...basically as you guys said, the rod was engaging the brakes all the time. Now i just need to re-bleed the lines and i should be good.
Brian Hobaugh SCCA National Tour June 2014
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