What I do for the tiny pits is to get a sharp pointed metal deburring tool to get down into the bottom of the rust pits. The one I use is in the shape of a Christmas tree. It cost me less than 20.00. The one I use fits into the right angle die grinder.
Rust will need oxygen and moisture to grow, and I don't think those specks are going to effect your paintjob in your life time.
I'd get the epoxy on it and move on.
Just my uneducated hack opinion.
how on earth do you guys keep from sweating on your work? this is getting aggravating. only way i can do any thing is frequent breaks or ill start to drip on my body work.