I am not familiar with the exact type of portlight you have in your Crealock, but I think you will find that laminated glass gives you the best long term clarity. After all this is what automoble windows are made of, and they don't cloud up. Plexiglass and other plastic windows have a limited lifespan, as they tend to craze from long term UV exposure. A pricy alternative would be to use tempered glass.
I assume the frams of these ports are bronze, in which case you don't want to use brass screws, rather bronze would be the right choice. Stainless would work, but be sure to galvanically isolate them from the metal of the frame using Tefgel.
For many applications in portlight sealing the best sealant is the butyl windshield caulking available from auto parts dealers. It comes as a soft, somewhat sticky cord. Details would depend on the exact material and design of the port.