Looking at that right rear 1/4, there is some previous body work that needs to go. This looks like a lot of work. If I were you, get a grinder and a flapper wheel, take all the rust off, down to the metal. Get rid of all of that body work on the lower right quarter with a screwdriver and a hammer. I bet it is rusted underneath, which is why it's flaking apart.
The best thing to do is get all the old body work and rust off. Then, I would clean with a good wax and grease remover, any left over rust could be treated with POR 15. Next, reshape with fiberglass body filler over the large, deep patches, then fill the smaller areas with putty/bondo. Sand till flat with the a DA sander, then clean again, then you can mask off and get ready to spray your Gatorgaurd, or which ever product you decide on.
Good luck, I'm doing much the same with my Cherokee, I'm dragging my a$$ on it cause I know it's a big job to make it look good.