Well, I know it's a lot of work, I have been doing restorations for 34 years. The problem is (as stated above) there is a good chance that there is rust under the epoxy that you can't see because it hasn't came through the epoxy yet but it is still there. It would be best to start over because not only is paint and other materials expensive but you have to factor in your time to redo the car again when the rust starts coming through your paint finish.
I don't know what you have for paint/material supplier but when PPG went to the DPLF series epoxy years ago ... I didn't like it's characteristics and I was talking with a PPG rep and he said that the OMNI epoxy works like the original DP epoxy and I experimented with it and it does work very well. I do not like the OMNI paint at all..it is cheap/poor quality paint.
You can use the cheaper sandable primers that each paint company makes, it usually sands well but it does shrink. So I would use a quality sandable primer and make sure that you read and follow all the paint manufactures instructions.
If you have any other questions, please feel free to ask.
Note; Picture is of a customers car that I am restoring now. 72 Road Runner 451 stroker 4-speed dana.