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Re: Replacing windows by adhesive & Butyl tape?
"however twice the size as you suggest would not hold the screws."
That's correct, which is why WASHERS or large diameter screw heads may be required. The size of the hole has to be made to accomodate the expansion in the sheet ofplexi. If that is 1/16" per foot and you have a three foot long sheet, you may need 3/16" of free space--even if your screw's body is only 1/8". The size of the head may or may not cover that. Basing the size of the hole on what size screw heads were randomly available, is setting the cart before the horse.
But as you say, you're not going to marry the boat, so if the windows are leaky when you go to sell it, or the next buyer sees a job not done right...all it affects is price.
WRT neoprene gasket, be aware that there is "chemically blown" foamed neoprene, and "gas blown" foamed neoprene. The gas blown type is "fizzed" with inert gas to form the foam. The chemically blown type is made like a pancake batter, chemical reactions make it foam up, and if anyone has cheated on the chemicals, it may turn to goo or powder down the line. Sometimes five years, sometimes twenty. So caveat emptor, you can guess which is more expensive.
So a quick simple fix, I'd just use 3M's VBT(?) tape, the structural double-sided tape that is used to secure windows in skyscrapers. Apparently works very nicely on boat glazing as well, and doesn't require holes or hardware.