It depends on how deep the pits really are. If they are more than about 5 thousandths deep, I would recommend using a two component finishing putty. I have used "3M Flowable Finishing Putty" with good success. This stuff is really the same as polyester filler commonly referred to as "bondo" in a more liquid form. The red lacquer "spot putty" will also work on shallow pits, say 5 thousandths deep or less, and I have also used it with good success. There are many now-a-days that frown on the lacquer putty. The problem is it will shrink some and the tendency for many is to use it to fill low spots that are really too deep and then not allow enough time for complete drying. It should be restricted to no more than 5 mils (thousandths) thick per application with liberal dry times between applications. Either the finishing putty or the red putty can be applied over your epoxy primer. Paint can be applied over the sanded fillers, however, I would recommend that you apply a couple of coats of a primer-surfacer as a step before final sanding and applying the topcoat. If there is any pitting at all still noticeable, just apply more primer-surfacer and sand until all is gone. Even very small imperfections at this point will be noticeable after the topcoat is applied.
You made a good choice to go with epoxy primer. That is about the best bare metal primer going, IMO. The one problem you might have that I thought of is the recoat time for the epoxy that you already have on the parts. The epoxy primers that I am familiar with have time windows within which they should be topcoated to assure proper adhesion. This time varies with the product...I have used one epoxy that had a three day window and another that had a seven day window. After the window has past, the epoxy should be sanded and re-coated with itself prior to proceeding. If you are past the window for your product, it is going to be just about impossible to rough up the surface well in the bottom of the pitted areas. If this is your case, I would recommend doing the best you can with a coarse "scotch-brite" pad and adding another coat of your epoxy primer prior to doing any filling.