Epoxy primer without a doubt. Self-etch primer was fine when epoxy didn't come in rattle cans but now its outlived its usefulness. Epoxy primer first then do all your bondoing, that way you don't have to worry about any exposed bare metal getting a flash rust. The epoxy with bond to bare metal better than bondo - particularly if the bondo is really thin like a skim coat. Also, looking at bare metal with all the scratches and scuff marks can be deceiving, the primered surface will give you a better view of what needs work.