Hi t3rra,
If you've got a copy of All Torque Issue 77, pages 20 and 21 go into great detail about the operations of the sunroof and repairing them. If you don't have a copy, click the link below.
http://issuu.com/tipec/docs/all-torque-77-issuu/21Unfortunately, the sunroofs are very complicated for what they are. I service and repair anaesthetic machines for my living and they are less complicated than the 944 sunroof! It sounds like something isn't quite aligned causing the cogs to strip after replacement. I hope you find the article useful.
Ben
