What should I do for now?

I understand muratic acid will continue to eat at the metal, never can really neutralize it. apppearantly phosphoric acids can have a problem with some primers. I've used metal ready and acid wash made by DuPont with good results, but I would always spray primer on test strip to be sure..
several body men here swear by self etch primer on first, them epoxy. you put filler directly on the epoxy primer, the epoxy primer can also be used as a sealer. then over that a high fill sanding primer. epoxy isn't made for sanding and leveling. that's what I understand....
if me I would sure d a it down good and then use some type of rust killing acid or a suitable rust killer. body men here don't like the rust neutralizing products, but hey that booger needs some serious something, good luck, it will be awesome!!!!!!