I had a problem with my top molding. The windshield was mounted 1/4" too low, so there was a gap that was a bit too wide for the molding to fill. The side molding was also coming up a bit. As a result, there was really bad wind noise from 45mph and up.
I tried 3M Weatherstrip Adhesive (not the "super" variety because it's more aggressive and seemed like overkill), but it just made a mess. It's basically black gooey contact cement that will never dry once it's sandwiched between 2 parts. It's really stringy and messy, and it's hard not to get it on everything like the glass and the paint. It seems to clean up with Windex and some scrubbing.
I ended up just filling the space with silicone caulk. That finally took care of the extreme wind noise I was getting from that area, and hopefully it will keep water out because it leaks a bit at the top. Whoever installed this windshield for the previous owner was an idiot (they also scratched the paint off the front of the roof. I don't know who installed it).
It looks like the windshield is glued in to the opening with clear adhesive. Then there is a thick bead of black adhesive on top of that that the weatherstrip is pressed into. If I pulled mine out, I wouldn't be able to get it back in. But I don't think the 3M stuff would work in that application because it would make a mess and never dry.
The "super" 3M stuff might be worth a try. Silicone caulk is not typically used for this, but I can't think of any reason why it wouldn't be good. Be aware that if you put it on too thick, it might not dry, but it seems to be better than the 3M adhesive about drying.
