Amervo, my car came from Southern Virginia, almost in North Carolina. I didn't find anything suitable closer to Maryland. The previous owner had already removed the windshield and backglass for repairs once. He nearly filled the glass channel with sealer. I'm told this makes it rot faster because it traps even more water when it fails. There's roof flashing under my windshield. I'm almost afraid to look. It has very solid rockers and floors though. That's a good start.
Joe, your leak probably is rust under the rope seal somewhere. The rope seal itself doesn't seem to dry out. By that I mean it's a tar-like substance that really sticks well. If it's sticking to lifted paint there will be rust underneath it. On mine, the window came out very easily because the tar was sticking to rust almost of the way around.
Amervo said if you leave a spec of black stuff in there the rust will come back. Let me add to that. If there is a hole through to the back of the metal it will also come back. If it has a hole through the steel, it should be welded closed or moisture will eventually get in from behind. Bondo has a bad reputation not because it's a bad product, but because the procedures used to involve poking a hole through the metal to pull out the dent. A small hole can be brazed shut. A large area, it needs to be cut out and replaced.
I wouldn't use POR15. I don't think there is any substitute for bare steel and modern epoxy primers. Fresh paint will cost plenty and you won't want a failure. If you do a full repaint, both the windshield and backglass really ought to come out. That way you get the glass channel cleaned down to bare steel and epoxy primered. Preparation is more important here than anywhere else on the car.
If you find a lot of rust in the tulip panel, the reproduction part is actually fairly nice. It's one of the most satisfactory aftermarket panels I have seen. If you need one, you want the one that includes the interior window frame. The tulip panel is not all that hard to cut out either. It can probably be glued in with the new two part 3M panel glue, but you didn't hear me say that.
Amervo, have you considered media blasting that spot instead of grinding on it? You would lose less metal thickness and it will still be squeaky clean. Evercoat Rage will fill in the surface texture pretty well.
