With the jumpers hooked up to the FFE 12v battery, the dome lights and dash should light up when you open the door. The 12V battery powers the circuitry for the charger so if it's dead, plugging in the FFE will do nothing as you observed.
The car cuts power to the USB a minute or two after you turn off the car and close the door. So no, leaving a thumb drive plugged in will not cause a problem. It really should have sprung to life when you hooked up the jumpers
Did the jumpers spark at all when you hooked them up?