From 1996 Ford CD,
Motor Synchronization (Timing)
If the sliding roof panel motor is removed from the vehicle, it must always be checked for synchronization before it is installed. The sliding roof panel motor is synchronized when the switch tab is in cam notch. If the sliding roof panel motor is not synchronized, remove the sliding roof panel motor as outlined and adjust it as follows:
1. Note: The roof opening glass should be in the CLOSED position for synchronization.
Connect sliding roof panel motor wiring connector to sliding roof panel wiring connector.
2. Hold switch ON until sliding roof panel motor stops automatically.
3. Disconnect sliding roof panel motor wiring connector from sliding roof panel wiring connector.
4. Note: When installing the sliding roof panel motor assembly to the sliding roof panel, it may be necessary to turn sliding roof panel motor assembly slightly to engage drive splines.
Make sure that the roof sliding panel guides are aligned. Connect the sliding roof panel motor and install to roof panel.
Edit. And if you removed or intend to remove the Moonroof Glass Panel,
http://www.contour.org/ubbthreads/showflat.php?Cat=&Board=genmods&Number=1097609&fpart=1&PHPSESSID=