You may want to yank the windshield and cut the A-pillers on both sides, then cut as far back as you need to on the center T-channel...The drawback is you'll have to find the new part from a pretty clean t-top car. G-body T-top cars were notorious for rust in these areas, but there are clean parts out there...I'd check the local boneyards, gbodyparts, or bweavy, and see if you can locate what you need BEFORE you start cutting anything.
I would also check the area in the door jam, just under the windshield piller, for holes or rust. A Monte T-top I had once had a rust problem on the roof, behind the windshield, and moisture seamed to go inside and work its way down the inside of the piller(where there is no primer, just bare metal), collecting at the lowest point. It had nowhere to go, causing a bit of cancer there also.
I am currently putting a 84 Regal limited together and encountered rust holes in this spot in the jams also, and this is NOT a T-top car, and doesn't have any exterior rust issues on the roof(or around the windshield), either!
Anyway...Check the jams!
Keep everyone up to date on your project. Hope this was a little help...
I read this quote in a book once:
"There is no way to stop rust, there are only ways to slow down the process of corrosion."