You may be better off using the other port light for a pattern and having a couple made up locally out of thick Plexiglas. Mine are held in place with wood screws. If your's are held the same way, you should make sure that you bore the holes a shade wider to take into consideration the temperature changes which can cause them to crack at the screws.
Also in my opinion, Dap Silicone Rubber Adhesive Caulking would be my first choice for caulking and adhering plastics. Just clean the area good and it will stick. You could use denatured alcohol for the cleaning. Don't use Acetone.