It sounds like you would have already checked everywhere for leaks, and the fact that everything worked for some time would suggest the install was done correctly. It does seem like a hydraulic issue to me and replacing the clutch master was definitely a step in the right direction. Do you have a separate clutch reservoir? Have the supply line and elbow been changed?
I also have a 2012 GT with the MT82. I replaced my clutch and related parts at around 70k miles, just this past September. I had a similar issue just prior to replacing the clutch parts and replacing the clutch master (Ford part) seemed to solve it for me. At that point, although things were working fine, I decided to preemptively replace everything. I have put about 500 miles on the car and so far, it feels great.
These are the parts I used:
Ford Clutch Master
Ford Performance Billet Steel Flywheel
Exedy Mach 500 Stage 1 Kit (clutch disk, pressure plate, pilot bearing, and hydraulic release bearing)
I also installed a new stainless-steel line, a new elbow, and a separate clutch reservoir.