POR 15 will stop the rust, it leaves the metal with a ceramic like coating. As long as loose or flaking rust are removed from the surface, an application of POR-15® will not only cover up the rust and prevent it from spreading, but will also strengthen the underlying metal and seal holes by forming its own membranes.

 

Just to update, I ended up getting this done finally..

I did end up sand blasting the pinch weld. I taped off the windshield opening but still managed to get some blast media in the car lol. I then hit it with a 2k epoxy prime made by U-pol. Put down a triangular bead of urethane adhesive and set the windshield.

The windshield trim did not come with the windshield, so I bought one from Team Cherokee.com. I would recommend this one after reading so-so reviews about others on amazon. Fit real well with a nice wide rubber flange.

Also did the headliner while I was at it. All in all quite a bit of work...