When you are installing new motor assy., you have to make sure that it is synchronized. Manually close the roof (turn the main shaft with pliers etc, careful around the serrations on shaft). Hook up the motor to the power, but don't install on shaft yet. Press the switch and motor should run then stop automatically. The motor will run for alonger duration when retracting than it will when popping up theglass. Make sure the motor is in the stopped position for closed roof. Not sure if this is really clear, but hope it helps. If you've got the Ford Manual, see section on synchronizing moonroof motor.
