Butyl tape is great stuff for sealing and bedding deck hardware. If the port has to open, and the plexiglass is part of the section that has to be removed, then use a neoprene gasket instead, as it is a lot less messy to open and close repeatedly.
As for the ports, I"d like to see a photo of the exterior before commenting.
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You know what the first rule of sailing is? ...Love. You can learn all the math in the 'verse, but you take
a boat to the sea you don't love, she'll shake you off just as sure as the turning of the worlds. Love keeps
her going when she oughta fall down, tells you she's hurting 'fore she keens. Makes her a home.
—Cpt. Mal Reynolds, Serenity (edited)
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Still—DON'T READ THAT POST AGAIN.