Hi LDM,
If you are still working on the lites, the overriding concern is the old sealant you have or will encounter. When I had that problem with my h23 the silicone bedding was very thick and twice as difficult to remove, mostly due to inconvenient working position. Also I had rubbery chips and slices of the stuff all over. Installing the new lexan, choose a sealant which will adhere to lexan. Sounds simple but anything short of butyl rubber may not permenantly adhere. If you have used it before..... nuff said. If not, then work very precisely and clear your work area around the lites. It's impossible to contain the stuff if your attention becomes divided. Install screws lightly after the butyl rubber has set up. With butyl, screws probably aren't structurally necessary. You'll find lots of other good advice if you search the forums. Oh, also look at a product named Lexal. I recently found it at Ace Hardware and was told it will adhere.
Question.... Why are you considering oversizing the lites? Is there a fiberglass lip around the lite that is recessed to accept the correct sized piece?
Best regards.... Rich B