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.
Tobin
KORE3
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