Sometimes some crazy electrical things can happen when system voltage gets too low... Use a multimeter and see what your battery voltage is at with the engine off, then start it up and see if the alternator is charging. A properly charged battery should yield about 12.7 volts, and with the engine running you should see 13.5 or more. Also check your grounds to the frame.
2013 F-150 EcoBoost MaxTow, Roush tuned (415hp 506tq), lifted on 33s, R.A.S.
2013 Jay Flight 28BHS Elite (Equalizer 10K hitch)