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In a similar case, I used an angle grinder and other weapons to clean up my cast iron keel. Then used POR 15 as the first coating. The POR stuff doesn't seem to care if there is some rust on what it is covering, so it seemed like good stuff to use when the timing couldn't be controlled. Do a google for them, some automotive paint suppliers will stock the stuff.
After the POR I used west epoxy and the appropriate filler to smooth things out. Sand, repeat, sand, repeat, etc. Then a final couple of coats of unfilled epoxy just for kicks. Lightly sand, repeat, etc.
It's only been two years, but the repaired areas show no sign or recurring rust.