I would start out sanding it all down to bare metal in the problem areas. For this I would start out with a DA sander and 150-ish grit, if there was still pitting, I would just get gradually more aggressive until you have gotten it all out. Maybe move to 75 after the 150, then down to 40. If that doesnt get deep enough or take off enough metal to smooth out the pitting, there is a fibrous wheel that is sold to use in drills that will be a little more aggressive than the sander. But dont use it around tar-like substances because it will gum it up quick.
While its still fresh bare metal, I would wipe it down with degreaser or a metal prep.
Put your featherfill to the bare metal(I would hit the bare metal with a 40 grit to rough up the surface as well for good adhesion of the feather fill), and level it all out where you want it.
To have good adhesion of the primer to the filler, start rough and get lighter with the grit of the paper(while leveling the filler), and I would end with 400 grit.
Etch primer over the featherfill, not sure if a second coat is needed, or what any advantage would be of a second coat. But since rust is an issue, I would consider it if there were any advantages.
Assuming everything is already level from the featherfill, shoot your paint. Then if you decide to wetsand the finish to make it really smooth, then start out with 500-ish, then move to 600, 800, 1000, and 1200.
Disclaimer, I am just a hobbiest, I would consult Ryoken for the final authority on this subject.
Also post up the progress pics of the fender when you get to work on it.
Remington