Terry,
There is a thread somewhere on here, but in summary - I used Lexan Marguard - bought from a supplier on Ebay - in 6mm (I think)
This is is the stuff riot shields are made from and is as clear as glass but 200x stronger and is scratch resistant.
I took off the old windows as a template, rough cut within 2/3mm with a slow fine jigsaw (to avoid melting the plastic) and then clamped the template to the rough cut and used a laminate trimmer in a router to get an exact cut (it's a little tricky but doubale as you need to ensure the roller sits on the thin old window.
I think I also put a 45deg bevel on the ouside edge.
Thats the hard bit - I didnt bother bolting the new windows except for a couple on the side windows to ensure they bend slightly around the cuddy, I just bedded them in on a bed of black sikaflex.
Hope that helps.
Adam