Getting your sunroof to pop up correctly is a very easy fix.
The following instructions will help you get your sunroof operating properly.
Remove the headliner:
Instructions for removing the headliner can be found here .
After your headliner is off, you will see four nuts in each corner of the sunroof. These are the sunroof adjustment nuts. They are easily distinguished by the rather odd-looking silver washers behind them.I would concentrate on the rear ones for the adjustment. try loosening them both slightly, and them see if the roof will open correctly. you will get it working perfectly thru trial and error with the adjustment nuts.
If you're going to have your headliner recovered, it is also a good idea to have the inner sunroof panel recovered to match.
To remove the inner panel:
Move the sunroof to the vent position.
From the outside, starting in the front, gently pull down on the inner panel from the sunroof panel. There are eight plugs that hold the inner panel to the sunroof. The plugs look like Parcheesi game pieces.
If you're feeling really frisky at this point, get back in the car, and remove the six 10MM nuts that attach the sunroof outer panel to the sunroof assembly. With this off, you now have complete access to all the mechanism on the outside. You can use a shop vac to remove all the debris that will be in the rear section (this part is never fully exposed, due to the fact the roof does not open fully, by design), helping to avoid plugged drains again. Be sure to also fully lubricate the tracks, hinges, pop-up mechanism, and air deflector assembly.
Your sunroof will now be working like new.
Thanks to reattadudes, member of the Reatta forums, for this information.