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I just finished painting my 1969 16ft Nauset. I'm going to be re-installing the bow rail. The previous owner had taken them off, filled the holes, and painted over them. Should I mark the spots where I will need to screw into the top of the gunnel and then drill/fill the holes with epoxy to create a base for the screws to anchor to?
You are over thinking it. Predrill and counter sink the top of the holes. Use a drill bit the same size are the screw shaft.
You could use 5200 on the bases to helps hold the bases down. And dont over tighten when first installing. I would worry more about hitting the old holes and finding compromised glass from the old screw holes.
If you do epoxy fill, the fill would go under the glass in the foam area to compliment the hold. Not on the glass itself. Epoxy filler by itself is not very strong and will probably crack when you put a screw in it. Putting the epoxy under the glass with act sort of like a wall anchor in sheet rock but is a way bigger process than what you described.
Archie