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Be careful with a “professional” glass installer. Most times they are the reasons for the rust!
I would use a rust converter. Then coat it with DOM16. This is meant for rust and bare metal. Then you can scuff it and they can use their windshield primer for the pinch weld.
That far up you could use something like a jbweld or and a seam sealer to cover those tiny holes. The urethane will be about where those letters are so no concern about that. If that's the worst you've got you're in good shape.
Any paint that's applied to this surface needs to be done like the factory would. Not just a simple rattle can dusting. The adhesion of the paint is critical since the urethane will be bonded to it. May wanna have a body shop prep and paint it for you.
Just to follow up and end the thread. I got the windshield in the day before Thanksgiving and used the truck for a little Thanksgiving travel. It was a bit of a last minute flail to make it happen. I tried to hurry the process by painting coats to thick and not waiting long enough between coats with bad results. I spent the day Monday driving back and forth between work and my buddies garage every couple hours and recoating parts of the roof to get good protective layers in place. It's definitely a 10-20' job, but it's done and should provide a good sealing layer to prevent future outbreaks.
One of the other lessons I learned is that blue painters tape isn't the right thing to use on auto finishes. It soaks up the new paint and then peels up the paint underneath when you pull it off. That sucked and is most of what made it a last minute deal.
I wish I'd seen this topic earlier. You were on the right track in post #17. Blasting it out is always better than any miracle brush on converters, and pinch weld primer will NOT stop rust in it's tracks.
My concern is that not allowing thick paint to cure through could haunt you later. Assuming that the urethane does it's job and bonds to the primer, you could see the uncured material you applied turn loose and stay bonded to the urethane primer. That will result in water leaks if it does happen.
Good luck with the fix, I hope it holds up!
The windshield frame itself wasn't a problem. I had a few spots on the roof and used blue tape to mask them. As careful as I could be removing the tape, it just took the old paint with it. The last minute flail was getting the roof fixed. The area where the urethane goes should be fine.
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