Not sure, but it sounds like drive cable/gear combo are not meshing properly. If I remember what I saw in my repair manual, the drive mechanism is in the trunk and the cable feeds to the right side of the panel. It looked like a long worm gear with a follower on the panel edge. I don't want to say too much b/c I am not really sure about how the mechanism works when in motion. I have also heard that sun roof repairs are a PITA to do. Maybe Donnie or Steve have some useful info for you. If a corner droops, then that's where I'd start looking. Maybe the right rear edge of the panel is out of the track. Good luck with this one..
1987 BMW 325