What to do????

Since you have rust in a couple of places, i would replace it rather than repair, especially if you have a cheap donor. The time it would take to blast, repair, bondo, prime and sand would be, well a while.

Cut the donor roof as low on the pillar as possible, bottom of the window frame, doesn't have to be pretty at this point. Get as much metal as you need to get below the rust. Set aside to cool.
Get some measurements from either vehicle for the openings, top to bottom. Write them on the donor roof in permanent marker or somewhere they won't get lost....
cut off the old roof just below the rust or at the factory seam(back) if possible.
measure, measure, and measure the roof and mark where you need to cut. The front is relatively easy, since it is small. leave an inch or two extra in the back to overlap if you don't use the factory seam. Set the new roof on the rough opening, and start trimming to the proper opening. (the back has inner panels to, and some bracing to the wheel house sometimes- easier to find where they join and cut, rather than trying to butt weld or overlap).
measure again, tack in place and paint.
Yeah, made that sound easy. ; )
Don't make it harder than it is, it's just another body panel!
Whistle while your doing it, that will relax you and you'll think you know what you're doing.