I'm in much the same situation, finishing off my TR4A body "tub" and getting ready to prime it with epoxy primer. I'm planning to sand off the paint, clean the surface, and prime it immediately. The problem is rust in pits, which won't sand off, and rust in places that are inaccessible for sanding.
I tried a number of things, and eventually decided to sand off whatever I could and abrasive-blast the rest. I hate blasting, as it makes a mess, but it definitely does the job. I may use some phosphoric acid where appropriate. If you do a little research, you'll find all kinds of stories about poor paint adhesion after using phosphoric acid, but I suspect that the problem is really inadequate clean-up. Just wash the surface well and make SURE it is dry, and it really should be OK. The iron phosphate coating it leaves on the metal surface should provide good adhesion. But, it also leaves open the possibility of rerusting in spots that were not treated.
My remaining dilemma is a couple places where there is rust, but it is not accessible to blasting. In particular, under the front valence and inside the cavities for the tail lights. I will have to sand these manually; should be a real pain. I am considering putting some rust encapsulator on those areas, but then I don't really know how well that will work with the epoxy primer. But, at the same time, I don't want to prime over a previously rusty surface that has been minimally derusted.