If I remember correctly there is a TSB out on the clutch pedal sticking problem. It is very common on GT/Boss cars. The solution from ford was to replace the pedal assembly with the GT500 assembly. Realize it is too late for that as you now have other stuff broken but just FYI Good luck.
2013 GT premium, Deep impact blue, Recaros, Manual, 3.73, Gt500 mufflers, Barton shifter, Steeda 91 tune, Pilot Sport A/S 3