Yes, you can order a roof with a glass rear window from our host. I would recommend it since it will end the issues the the plastic rear window forever. I replaced the roof on my '02 Boxster myself, but budget a full weekend or 2 for doing it. It's a little finicky, but the instructions in Wayne's book, and the expanded set of pictures on the Pelican site are definitely useful. The only thing that is not covered real clearly in the instructions is described
here.