You could have a new piece of wood cut and carved to match so that you could replace the bad piece with it.
Then use a piece of sand paper to smooth it down by-hand and stain it after it's in-place. You'd probably have to re-stain all of your wood to get it looking good and even throughout, though.
If you have water
coming in from outside, you'll probably have to open a whole other can of worms to repair it. Such as possibly pulling the chain plates, cutting out any bad or rotten wood/fiberglass and replacing it with new material.
It sounds to me like it could potentially be a very time-consuming job, especially if you aren't familiar with the process of repairing fiberglass
or wood to a marine-grade finish.
Might be a good idea to talk to a professional about what it would take.
There's a youtube channel called "Sailing Uma" that has several great videos about repairs
they have had to do to get their boat ready to go back in the water
This video gives you a basic idea of what you have to do to properly take care of a chainplate problem, even if it's only a small leak. Its safe to assume that if there's already a leak, then there's also already rot and moisture-related problems around the chainplate hardware
under the deck
Anyway, I'm not
a professional, but I hope this helps.
And I'm sure there are several old salts who could give a lot more helpful advice here.