assuming that the EB3 checks out to be working, I think it would be safe to assume that the problem is the PWM module. Correct?
I would strongly advise that you attempt a ESC calibration. This bypasses the flight controller completely and sends the power from the lipo, through the pwm module and into the ESCs, directly. If the motors spin properly, then that rules out short cirucuits or damage to the pwm module.