Be careful about replacing the plastic with glass. Convertible top designers generally would like to use glass instead of plastic but are limited by the space required for the glass to occupy with the top open. If you're considering this option first glue a piece of plywood/plexiglass to the existing plastic and cycle the top several times and look for clearance problems and anything that may contact the glass during cycling or when the top is open and you hit bumps in the road.

Good Luck !!

 

There is a little known service bulletin that allows a dealer to put in a new one for free. There had been some discussion of an NTSB alert about the windshield in the early ..........going back to the early days of the board. The bulletin was to be performed at "the dealer's discretion" (READ BE REALLY, REALLY, NICE). If your car is an '00 send me a PM. I'll point you in the right direction.....the bulletin applied to '00's only. Before I get 100 emails on the subject this reply applies only to the author of this thread....maybe he'll help you out later as this subject has died out for a while!!!

Utah

 

I think that my plastic rear window is not creased because I always park the car with the top up.
I also park mostly in a garage, or at least try to park the car so that the plastic window is facing away from the sun for the duration.
Plexus Plastic Cleaner works quite well when the window gets clouded, while I've used stronger products to remove the initial scratching.
I purchased some black felt with adhesive backing, and lined the rear shelf with a two-inch strip where the plastic window touches. This has stopped further scratching after I polished out the initial scratches.