Who could I contact to have a piece of polycarbonet or tempered glass cut for the Decklid window? And would it be a good idea to bring the cutout from the lid as a template?
Any specialty glass shop can create tempered glass. When I worked in a school bus shop I had a local glass shop cut all sorts of tempered rectangular flat glass pieces. You just need to call around and get quotes. Prices will vary but are typically in the $40-$150 range a piece.
I would not use the cut panel as a template. Glass needs to be very exact in it's edges in relation to the rest of the body and where it mounts. If I were doing it, I would make the cuts, clean up the body around the hole and smooth it out, go to Home Depot and get a cheap sheet of polycarbonate lexan, cut it to the exact shape, and then use that as a template. You're going to lose some material from the body with the cuts and that piece that's left over won't make for a good template.