It seems you're indicating the doors will open and stop correctly. Since power is getting to the motor to open, this would indicate the problem is in a relay or the headlight switch. possibly a disconnect or bad contact depending on the degree of hacking done on your system. My switch has been a little screwy lately with having to make sure it hits the detent for closing the doors. Having reworked my RS doors, I would have to say a relay would probably be the bet based on what you're saying. They are neccessary to get the voltage on the motors reversed until the limit switch shuts them off. A voltage meter should give you an idication of current flow.