I would weld in the patches, strip the entire panel to bare metal and epoxy prime with a gun designed for primer.
Doing it this way will allow you to work on your truck piecemeal, one entire panel at a time. When you are done with each panel, the entire panel will be protected and you will have a very good base to begin with body filler, and another coat of epoxy primer to protect the body filler for final block sanding of the entire truck.
