I have done a lot of searching on troubleshooting the 2nd gen sunroof and why it will not close all of the way, won't open on it's own, etc. etc. Well, I finally had the opportunity to replace mine yesterday and realized it could have been an easy fix if it had not been for the rust in the sunroof tray letting water in. If this is common knowledge, sorry...I have just never seen it posted before.

If you have replaced your sunroof and it will not close all the way you need to take out the headliner again. On each side of the sunroof there are 2 bolts that bolt to the frame and two nuts that have 'c' clamps under them. Loosen the two bolts on each side and the four in the back. Then loosen the 4 nuts (the ones with the 'c' clamps, this lowers or raises sunroof to appropriate level). Since the 8 brackets are oval, you can tighten the 8 bolts and the sunroof will stay in the right place. Hope this isn't too confusing and it helps somebody.

~Rob