I've searched rust to death, need experienced opinion

[nail pounder]

How do you deal with pitted rust? I've read everything on the net, I was all set to get some ospho but then read about bad reactions with epoxy primer. I used those polycarbide disks to remove the paint & they work pretty good. I have rust pits under my bed rails (no pics) and some on the top as well. I'm just barely getting started on a long tedious process, this section didn't take too long, figured I'd pull the wheel tubs out and finish, epoxy it then start another section. Eventually it will get done. I'll try a wire wheel tomorrow, but how do you guys deal with this at home? Sending it out to blast is not in the budget at this time. Any tips on stripping the cornes? To be honest there isn't much rust on most of it but I'm hesitant of just stripping the yellow and shooting epoxy over the old primer & original paint. Maybe I'm thinking too hard.