I think if I was in your position, I would drill out the spotwelds along the beltline reinforcement and plug weld the new panel in place. That assumes that the new panel has the same flange that's sandwiched in place. I think that would be much less likely to warp than butt welding the new pane on that top 1" strip and trying to dress up the butt weld.
Thankfully, I'm not in your position.
It sounds like a lot of work in either case.
Good luck
