I have had to do those exact repairs. Lower windshield corner i actually fabricated myself. I had holes in the roof panel all the way around the cab near the drip rail as well as above the windshield. Replaced both the inner and outer roof panel. It actually went way easier than I expected. Run some interior bracing to keep everything squared away, keep the doors on so that you can make sure the new roof lines up with them, then just follow the factory body seams. You will need to drill out about 100 spot welds to separate the panels.
Do you have rust through all the way around the top of the roof? If it is just up above the windshield, they make those two patch panels now and you wouldn't have to do the whole thing. How bad are the A-pillars? if it is just surface rust I wouldn't mess with those.
Roof swap:
https://photos.app.goo.gl/T86g0LLLPL5nZyJs2
