Wondered how you planned to tackle this bit.
If it were me, with a good panel like you have to let in, I'd remove lower part up to braze joint on pillar and separate your cut out carefully and plug weld that in complete.
Then I'd sit and think for a few days....welding along roof skin would frit me to a frazzle, be tempted to tack it and lead load it, don't think strength is an issue with cage in.
Or, let sections you need to replace along screen surround at the top in, cut from your cut out, keep air on it, move about, keep heat down down....keep dropping bare screen in with some wedges to keep an eye on seal clearance, and at the very least test fit screen with rubber before you skim any pudding on it.
Best of luck!