just for clarification: Plexiglass is a product name, not the material, which is acrylic - this is used for the dodger windows of the SM. You bought polycarbonate, which is fine: more sensitive to scratches, stronger against impact.
If you use polyurethane for bonding (either a Sicaflex or a GE product), you will need some kind of UV protection for the sealant. Amel used a thin coat of gelcoat on the windows. To put it on you have to check with the manufacturer (of the polycarbonate), if there is any kind of wax/protection on the "glass", how it can be decreased and if you need to sand the strip of polycarbonate, where you will put the UV cover (first) resp. the polyurethane (later). For the polyurethane you will need some kind of spacers (like small rubber strips) to keep a certain thickness (about 2mm) of the polyurethane.
If you use gelcoat as UV protection, it will be sticky on the surface (if you don´t cover it with tape). Either sand the sticky surface or don´t bother, because you will use polyurethane afterwards.
If you use topcoat (which contains paraffine for getting a glossy and nonsticky surface) as a UV cover, you will have to sand it to get a good bonding of the polyurethane.
I´m not sure about what you mean with "5000" - if is it some kind of rigid adhesive with a thin coat, it might be difficult to make it waterproof.
Walter (Noa, SM2K #436)