Re: Wood shaft log
If the area is localised you should be able to rout/machine/chisel all the rot out and then scarf a new peice of timber into the space. Glue with epoxy or a recorcinal glue and fair the surface off. If you are worried about the structural integrity get a wooded boat building expert/surveyor to advise.
Scarfs are normall a minimum of 6:1. If its a fastening place only thats rotted, bore it out and glue a dowel in place.
If it means covering the whole of the shaft log, do it and machine/bore a new log hole. You might require expert assitance with that.
Make sure you use the same timber as the existing wood so that it expands/contracts at similar rates wih the surrounding wood. Try and keep the grain running the same way as well.
There's nothing much that can't be fixed on a wooden boat - its just that somethings are very very much more difficult than others.
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Wishing things away is not effective.