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Any of you guys put sealer or something behind those two cast adapters that the windshield pivot bolt rides in? Seems like there should be something there to prevent water intrusion. Like maybe plumber's putty or something?

That sounds like a good idea.

I would guess that a plumbers putty type of material would leach out its oils over time. I would use a premium grade of silicone or a non hardening Permatex gasket maker, to seal the bracket if it were me.

Bert

Of course this topic leads to the question: does anyone put a sealer on the floor panels and transmission tunnel? I'd hate to use something that is going to remove the paint or cause the panels to stick together such that I can't get it apart for repairs.

I really can't see the need to have a gasket in this location. The vehicles aren't the most weather tight. As previously mentioned, the floor area doesn't have any gaskets to prevent water from entering.
Maybe a rubber washer on the inside, like is used on electrical fittings.