I have started spending some quality time back up inside MaJic Carpet and have been sorting out various issues I plan to deal with soon. One thing that has my attention are the several places that the woodwork has become black stained from leaks in the deck, windows hatches etc. These aren't horrible by any means, but they are unsightly. As a woodworker I know these stains don't just sand out. So the options as I see them are:
1) Ignore them
2) Use a pigment paint or a very dark stain and paint the woodwork
3) Replace the stained wood
Am I missing any options?

Inspecting up under the gunnels shows both the toe rail and stanchion bolts are prime contributors of the moisture that caused most of these problems, so for sure I will address them.

Once you've sanded to bare wood, try cleaning with a "wood bleach" which is Oxalyic acid.

The best way to prevent toe rail leaks is after varnishing them , to use a caulk like 3M Marine Adhesive/Sealant Fast Cure 4000UV, 1/10 gal. cartridge. Even after the caulk peeled away, the leaks stopped. If you try to remove the bolts and re-caulk, you will destroy the toe-rails.

That may be a realistic approach to toe rail leak problem. My toe rails visually look ok and I know any effort to get underneath them means destroying them. But the leaks have to go.