Id probably use black or grey RTV silicone. Thats what I would have on my shelf, but I can't think of anything that would work any better off hand.

It seems so weird that such a place could exist. I wonder what other little leak areas there are like this. Could it be that originally that was just two solid panels butting up against eachother, and over time, the inner panel has developed some rust holes from the pooling water?

How hard was it to remove the windshield?

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