So far I have been spending most of the time trying to weather proof and halt the damage. The strategy is to remove the rust and then seal. The rubber is in pretty bad shape and when I replace that I will take more care with the paint. Till then it is all about stopping the rot and leakage.
I strip rust off and apply Rus-Mort on the remaining rust. Following instructions I apply at least four coats over at least two sessions till the rust is gone. The windshield took about four days to do.
I then clean the area and dry it. I then apply two coats of SelectSeal on a hot day. The end result is a thick epoxy like barrier.