Hi Tony
Having had a couple of 986 Boxsters, I know that the 986.1 (plastic rear screen) and 986.2 (heated glass screen) had different roofs which obviously folded slightly differently - you can't fold a glass screen like the flexible plastic one. It is possible to fit a glass rear screen in a 986.1 but it's not a like for like replacement of the screen and as you point out you need a whole new soft top roof.
I've used these people for my old 'classic' (MGF) - maybe worth a try ?
http://www.car-hood.co.uk/986-boxste...s-upgrade-h809