You need to deal with the rot first, or it might continue underneath
the coating you apply. a) You could apply a product called Termin8t
[something like that], which is a solution of copper naphthenate that
will kill any rot-causing organisms it contacts, and then coat over
that. b) If you are near a coast, you might be able to find some epoxy
coal tar coating in a marine supply store, and just apply that alone.
It is not allowed in inland water boats, though, and it is hard to find
sometimes.
In the good old days, there used to be a number of good compounds that
would do the job, but the enviroweenies and safety nazis have stopped
most of them.
Best wishes with your project.-Jitney