I would suggest you remove the windows and reseal them all. Much water comes through dried out window seals. I used spray foam in some areas that were double wall and inaccessible. You need to allow for some place for moisture to drain if you do that. Then as suggested coat all the bare or rusted metal to stop the rust. I am going to have the underneath of my fenders bedliner coated. Mostly to limit stars on the outside from rocks. Mine will be a daily driver.
