Since the weight of the cap comes down the sides and the sides are at the outside of the overhang I would definitely use a wood or aluminum or steel piece between the trailer bed rail and the cap. Otherwise I would fear that over (a relatively short) time the cap's base will begin to collapse and fold at the outside edge of the trailer bed. Wood would be cheap and easy, aluminum light and easy and thin. Maybe 1/4"x 3" strap cut to fit the sides and the front? If you go wood, you can skip the pickling and just paint. Either make your rear window long enough to span the gap or add a similar piece of wood to the top of the tailgate...
For a fixed window, I would use a marine caulk between the fiberglass of the cap and the plexiglass, clamp in place and then drill your bolt holes. Remove, apply caulk, put the plexiglass in place, clamp and bolt together. That way the caulk/sealant/glue will provide a seal. 3M's 5200 is a ploysulfide caulk/glue that seals well and remains flexible so it won't crack with vibrations. It's available in white or black. The downside to 5200 is that its gripping power is huge and if you go to replace the plexiglass you will have problems. If you foresee that, try 4200, I think very similar but without the tremendous grip.
I would hinge the rear window. You should be able to pick up some piano hinge from Home Depot. If you use wood to support the top on the trailer you could easily instal a latch on the wood on the tailgate to keep the hinged rear window closed. Since the rear window opening has a raised rim around it you could get decent sealing using self adhesive weatherstripping around the raised lip and relying on the latch to keep the plexiglass closed and to compress the weather stripping. You will need a thin wood spacer under the hinge to provide room for the weatherseal at the top of the raised lip. The stripping is cheap and available at HD or any decent lumber yard or hardware store.
Hope this spurs ideas.
JPK
