When I encounter pitting like that, I have the truck sandblasted and epoxy primed. Not just for those particular areas, but for addressing similar rust where ever there are pinch welded panel joints.
If that is not in your budget right now, then you can clean up as much of the rust as you can, then use Ospho, clean up the chalky residue after the Ospho is done with its chemical reaction (24 hours), then prime with Rustoleum Rusty Metal primer and paint with Rustoleum color of your choice.
This will stop further rust from occurring to that particular area until someone wants to do a complete restoration with media blasting/epoxy priming.
