I have owned a restoration shop for many years and I have dealt with this problem alot. You will need a trim tool to remove the windshield mouldings. I use a bottle opener to remove the driprail mouldings. The 1/4 panel mouldings will either need to be pushed up and the bottom snapped out or "rocked " back and fourth until the release. Because they will not be able to be reused, I have sometimes broken them off. Then the vinyl can be removed. I then DA the entire roof with 80 grit to remove the glue and loose scale from the roof. I spot blast the rusted areas or weld in patches if the damaged area warrants it. Finish the metal in the traditional way (lead, bondo, polyester putty or what ever you are comfortable with. I would then apply two coats of self etching primer followed by two or three coats of a high build epoxy primer. I paint the roof body color to keep the original look, but you could skip this step if it doesn't matter to you. Then I replace the vinyl itself. Sounds like alot of work, but it really isn't to difficult. I have used this procedure on many cars with no problems. I restored a 1969 hemi superbee about 15 years ago and the roof still looks perfect with no bubbling what so ever. Good luck....hope this helps.