I just replaced both rear rotors,pads and calipers. I replaced the calipers because the rear driver's side was too worn and thus hyperextended (Thanks previous owner). After replacing I went for a drive around the block. Things seemed pretty normal but when I pulled back in the garage, a plume of brake smoke surrounded me. I looked at the rotor and it was cherry red hot. The passenger's side was fine. Could it be the master cylinder? Both side's brake lines bled fine.

The master cylinder wouldn't cause that. Obviously something is dragging on that one rotor. Can you hear any noise from it? Check your installation to see if all was put back properly. Especially check to be sure that the caliper pistons are retracting and not holding the pads in constant contact with the rotor.

+1 to a caliper problem. Had similar on a prior Ford product and it was annoying as hell.