Welcome. The vent fins I would have hydro immersed like in the link below. Removing them is a delicate process. To replace them call a dealership or wrecking yard.
http://invision.aleromod.com/index.php?showtopic=9127
They finish will stand up to the heat better than paint.
I have no idea on the power windows.
The rust should always be sanded off as much as possible then for the wheel well inside i would use a rubber under spray from like walmart or something. good stuff.