My 67 had rot down in the rear windshield corners that was working its way up the sail panel. It also had a vinyl roof. As I grinded away the plastic things looked worse. It didnt look so bad before I brought it home and statred poking. My windshield channel was swiss cheese too so I ended puting in new NOS quarters. I hear different stories on the repo quarters. Maybe someone else will chime in. Check your lower windshield corners for lurking rust. Climb in the trunk and look up at the corners of the windshield and the seams between the trunk and the windshield. If the windshield channel is bad its a strong possability the corners are rough too. The full quarter replaces everything up to the roof seam. Alot of work drilling out all the welds, but it was worth it for me.
Good luck and if your going to do the work and have any questions about where all the welds are just ask me. I never did this before and it wasnt real real bad but it is work. If you do take the quarter off you will probably want to check the wheel wells and the trunk drop downs and extentions.