This has been discussed a lot in previous weeks. The number of people who have done the glass installation numbers in the single digits (probably only a handful), so solid info is kinda hard to find.
I'm in the process of doing the swap, here is what I've done so far (I dont have a lot of time, thats the main thing holding me back):
http://www.preludeonline.com//showth...=sunroof+glass
Here is the original thread in which the topic was discussed. You can see there is a lot of "first hand" experience with the install:
http://www.preludeonline.com//showth...=sunroof+glass
To answer your question, the solution seems to be removing the interior headliner, unbolting the ENTIRE sunroof assembly and reinstalling it with some washers between the frame and roof (essentially shimming the whole shebang downwards a few millimeters).
Did you just remove some of the mounting tabs on the 5th gen panel to get it to drop into place? I've heard you can also you the 5th gen brackets, but I just ground down four of the studs and the bumpstops