Hi Miriam,
I did all my portlights last year. The following was all for the round portlights, it might not apply for the rounded rectangles.
I took out a portlight of each size, busted the glass out of it, unscrewed the ring, cleaned it all up and brought it to a local glass shop. Turnaround time was a day or so for them to cut the circles for me. Install wasn't part of the deal.
The glass they used was regular clear safety glass, two layers with the film between them. I had 6 of each size cut (6" and 8"), total cost was a couple of hundred. I think it was $20/per for the large, and $15/per for the small - $210 pre-tax rings a bell.
Make sure the glass shop understands what you are doing. On mine they cut them all too big first time around. Leave a portlight with them so they get it.
While I had the portlight out, I had 2 mil clear poly over the opening, held on with a large screw clamp (or two small ones, biting each other's tails, so to speak). It worked very well and didn't leak at all. I'd get enough to cover two windows for each size, if you are doing an assembly-line process.
Last winter, on cold rainy nights, I just took off a couple at a time, removed the glass and ring, soaked it overnight in mild acid to clean it up a bit, polished the part you can see from inside and put them back in.
The trickiest part was getting the ring back in all the way and snug. I had a version of a pin wrench built - basically an aluminum bar with pins sticking out on either side, indented deep enough to fit inside the portlight. One side for the big rings, one side for the small. It worked like a hot damn. I spent hours trying to find the right tool online, and in local tool shops, but found nothing. Finally I just had it fabricated. The machine shop at the university I work at made it for free.
I used silicon on either side of the glass, but go easy on it. The first one I did I made such mess I went back to the glass shop and had them make me another. If you don't tighten quickly the glass spins around and smears the silicon. Another good reason for the pin wrench.
You'll need a hammer to smash the glass (I used a rock), a heavy duty brush to clean the glass out of the threads, thick leather gloves to hold on to the thing while you're working on it. A mild muriatic acid solution worked well to clean the bronze over night - but go easy on it. The bulk of the time for me was spent cleaning out the old sealant. It was very tricky. Came off easier after the soaking. Needed a small blade for that, like a razor, the bronze scratches easily. You'll need something to scrape the excess silicon off immediately after tightening the rings too. Razor again.
I'm just telling you the above to save you repeated trips to the store, assuming you don't have a fully stocked tool shed.
If you want me to mail you the little pin wrench for your project, let me know. Just send it back when you're done. I won't need it for a few years (knock on wood).
Stephen