Aloha John,
First, congratulations on making it to the Herreshoff Regatta in August, you made the recent issue of Current.
Steve is spot on, it is part of the patina that says Crusader has weathered more than just the years. Your 80 year old grandmother can still be beautiful, but you wouldn't want her wearing a teenager's get up, would you?
You might wish to consult the bible on wood refinishing, Rebecca Brightman's BRIGHTWORK The Art of Finishing Wood. Brightman covers mahogany, the different types, and getting rid of the black water stains. Strip first, repair joints and holes, remove or choose to live with the stains, seal, sand, first coat, sand, second etc.
Holes can be filled with epoxy thickened with wood dust from the coaming or other similar wood taken down.
Generally, the mahogany doesn't like to give up its stains. Good luck.
