I'm right behind you on the alpines with sunroofs as well. I'm doing the following:
1, Pull out seals using care, solvent whatever. Hopefully reuse some. Pull out windows
2, Sand/cut/grind away rust.
3, Treat with rust inhibitor.
4, Bondo up holes, hopefully not have to rivit. Sand/Seal. Prime
5, Paint Roof and hood scoop flat black
6, Gasket silicon all seals in position. Use string method to get glass in

I've never done it before nor have I slept in a HD Express or played bodyshop guy on tv.