A photo of the ports you are trying to replace would be helpful.
There is some debate on the relative merits of acrylic vs. polycarbonate (plexiglass vs lexan). See for example this article:
I spend inordinate amounts of time discussing the pros and cons of acrylic and polycarbonate. In so much as I would like to bring some clarity to this issue. Please consider the following: All major hatch, portlight, and window manufacturers use Acrylic in offshore / bluewater marine products...
hatchmasters.com
Use Dow 795 or Sikaflex 295 UV to bed and seal them. Screwing and bolting is not recommended. A few screws along the edge (not through the acrylic) can be used to support the acrylic until the caulk cures. The lens rests on the screw and the edge of the lens is captured under the screw head, use a round head or pan head screw.
While cars and boats have some similarities, there are important differences. Solutions for cars are often poor choices for boats. One area this is true is in the DC electric system. SAE wire is smaller than AWG wire and has fewer but larger strands. AWG has more strands that are finer which makes it more flexible and less susceptible to work hardening. You are wise to recognize that auto glazing has different requirements from marine glazing. Boats experience more vibration and the hull and deck twist and move more than the parts of a car. Sealants must be able to adhere, flex, and stretch on a boat.
5200 is an adhesive, not a sealant or caulk. It is often referred to as the "Devil's Glue" because it adheres so well, but it is fairly rigid when it cures and extremely difficult to remove. There are only a very few applications on a boat that requires an adhesive as tenacious as 5200.