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Water gets in the windshield frame in the header area, and runs down the "A" pillars and on to your floors. GM filled the area in the header, where the outer windshield molding and the T-top molding meet a with sealer like what use to be called "dum-dum". If you look at an AIM, you will see that the installation of this sealer was somewhat haphazard, and over time, it dries out and shrinks up, allowing water in between the moldings.
Many a 68-82 Corvette has been found with a rusted out windshield header, "A" pillars, cowl and/or floors, because of water getting in through this area.