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I used black ribbon caulk from NAPA - about $15 and enough to do a number of cars - use on top and sides of windshield and even bottom if required. Can also be used on t-top bar where there are open places.
Inside the channels of the upper part of the windshield frame is a putty type substance that completely filled the channels prior to me removing it.
What was it? Presumably it is to waterproof the windshield frame and T-top bar.
What can I replace it with? Is there a problem with sealing all the seems with silicone once I'm finished POR-15ing the windshield frame/bird cage?
Thanks!
Silicone will cause enormous problems for you - it should never be used on metal parts of a car exposed to moisture / weather.
The original sealers were either seam sealer or (in the area you mentioned) Butyl caulk, depending on the application. In areas where you might think Silicone, Urethane is THE choice.