Rot in wood comes primarily from fresh water intrusion, absence of light, warmth, and lack of fresh air circulation. Mold spores get in with the water, usually rain water through a crack, crevice, or poorly bedded screw hole that penetrates the wood.
Once the mold has found this optimum environment, it sets up home and starts to spread by way of mycelium, (threads of mold branching off from the parent colony). Your damp wood has become the food source for the critters. Sort of like microbial termites.
Now that you have a picture of what is happening, you are better prepared to keep it from happening again, after repairs are made. You **must** stop the intrusion of fresh water into the wood, otherwise, you'll be back to the same problem in a couple of years, (sooner if you are in a warm climate). Check every possible source of water seepage into your wood. Stanton plates w/ screws poorly bedded, cracks in the fiberglass that extend into the plywood core, leaks from hatches and ports, leaks from fresh water plumbing systems, etc.
Once everything is tightly sealed, by either repair, replacement, or re-bedding, you can confidently begin replacement of the rotten wood.
One of the most important elements in replacing the damaged wood is to assure that water can not be absorbed in the future. Epoxy coat every surface, especially the edges, of the replacement piece. Epoxy is virtually water proof and is not a desirable food source for mold. Another, although possibly more expensive route, is to replace with rigid PVC foam board rather than plywood. This is even the preferred replacement material for exterior upholstered items. Water is going to find its way in through seam stitching, holes, and even the porosity of the fabric. Replace all upholstered plywood with PVC. Seats, bolsters, the works. Solid wood members that have rot damage can often be repaired, rather than replaced. If the damage is not too deep into the surface, (usually the case), the affected areas can be scrapped away or dug out, dried, (couple of days open to air with a fan circulating it), or for smaller areas, with a hot air gun or hair dryer.
Once dry, build back the area with filled epoxy, or for larger damage, sistering in patches, using filled epoxy as the adhesive of choice.
Bad plywood should be cut back into the undamaged areas by at least two inches. Inspect carefully the edges of the cut out for evidence of mold. It will have a black color and even on dry edges there might be evidence of mold spores, (looks like black or grey dust). Also tap with a small hammer or screw drive handle, and listen for a dead tone. If necessary, cut back deeper into the good wood.
Once your cutouts are complete, use a spray bottle filled with a water & bleach solution and spray all exposed wood. Get it wet, not just damp. Let it soak for a few minutes and wipe off the excess. Let this dry for a couple of days under circulated air, and epoxy coat all exposed wood. Again, pay particular attention to sealing the edge grain.
Once you've fitted and epoxy sealed the replacement pieces, epoxy them into place using filled epoxy. Saw dust makes a good inexpensive filler for this type of work. Same applies for filling epoxy to build up solid members that have been dug out.
Doing all of this epoxy sealing will add about 50% to your labor time, probably 20% to your material costs, but will likely save you from ever having to do the job over in the future.
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Editor’s Note - We are saddened by the passing of our writer, Captain Patrick McCrary who created www.Bertram31.com, a space where owners and potential buyers could share tips and where he helped anyone who made inquiries with his vast knowledge of boat mechanics and craftsmanship. For more information about Patrick and his many adventures and accomplishments, visit www.Bertram31.com/bio.htm