Re: Cutting windows
A source I use for the polycarbonate is Plastics International
http://www.plasticsintl.com/ They carry anything you would want. Best pricing I've found. I've found that there is a HUGE price difference between distributors.
Lexan is a trade name, and there are many out there but generally they are all referred to as polycarbonate (some just have protective films to add scratch resistance and UV protection. The brand that I typically use is Makrolon GP (no scratch resistance but is UV stabilized). You can get the scratch film with any brand but IMO unless they are going to be mounted on deck where they can get foot traffic I don't know that it's worth the additional cost.
Also depending on the install lately I've been using an 1/8" VHB (very high bond) tape made by 3M. I use this to seal the glass to the frames and then a regular compound (4200 or 4000) to seal the frames to the boat. BUT, this isn't necessary for every application. If there is a caulking seam to trim off the exterior side of the glass and frame use a silicone. If you have a chance post some pics of your situation. If the glass is transparent (visible where it mounts onto the frame) the tape gives a nice clean appearance rather than using a caulk which may leave some "bare" spots allowing the frame to be seen through the glass after install (hint-hint). This is how many of the manufacturers do it giving a nice clean, trimmed off look. I live in north wisconsin where we get a huge swing in temps over a year and have never had an issue with bonding failure of the tape. Works very well, but I've always had to special order the tape direct from 3M to get this thickness and in black.
As far as cutting the material, I use a standard wood blade that cuts on the down stroke. Leave the protective film on the glass and run a piece of masking tape along the bottom feet of the jig-saw. I've done quite a few of these and have always had great results.
Hope this helps!
~BWT