Great stuff, nice detail. Do you need to cut the roof gasket? That wide part just extends into the cab and being in the back won’t be too noticeable. Just a thought. You might try a little heat from a hair dryer - not too much - on those weather stripping wrinkles and rub them down with fingers as you go. I’ve seen them disappear once the rig sits in the sun a bit.
I don’t know if you have already addressed this, but I would definitely recommend you use some paint coatings on the inside followed by some fluid film once everything is done. I can recommend Zero Rust. I use liberally and allow it to flow into all the crevices. It will help keep some of your rust from getting worse. The fluid film goes even deeper, but make sure your paint is well cured. Good luck.