I used 1/8" Lexan when I restored my HUP 30 years ago, have not broken any of them yet. What you are looking for is something that will really resist scratches as that is the biggest problem.
I'm not sure how your frames were done they appear to be of the 1942 or early style for the Pat 13.
My HUP is a 1945 so it has the four panel style. Originally mine had and edge rap of friction tape with the flap edges being canvas.
On my web site you can see the HUP windows fitted on my C60S which didn't have windows.
http://www.canadianmilitarypattern.com/Posting.html if you need more photos of the frame let me know.
Cheer