Can anyone advise me on treating my nail-sick strip-planked boat?

She is iroko on steamed oak beams. The planks have been fastened both
transversely and into the beams with ferrous nails (I think they are
steel). These are now apparently rusting, and pushing out the wooden
pellets filling the counter-sinking above the nail-heads. A few have
popped completely, many are just forcing the pellets up proud of the
outside surface of the hull.

Perhaps because this has been a long-standing problem, a previous
owner has epoxy-sheathed the whole vessel. Clearly it hasn't fixed the
problem.

How is this best treated?
Should I remove the pellets and treat the nails? What would I treat
them with?
Can I replace the nails in any way?
How would I make good the epoxy coating? Can I just patch it with
epoxy after making my repairs, or will this ruin its integrity?

Any thoughts would be really welcome.

Thanks,
Jess