Ok, heres what i suggest. For the rust, take it down to the metal. If you try and leave anything, it will just come back. Depending on how bad the rust is depends on how much you have to pull. From what it sounds like, i would do all the fenders off from the vehicle. then blast the inner wells, and prime/spray accordingly. As for your vinyl roof, you can un-attach your roof, remove the rust, level it out and glue(literally) it back on and not one would be the wiser. However, if you want to remove it, it can be done. The best method ive found is to roll it off as one piece if you can get away with it. Then get some glue-remover, seal any holes/drill spots, and paint as needed. As for painting, you need a gun, a Good compressor and a clean area. Also, a Air Mask is a must. Nothing worse then breathing paint fumes.