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I don't want to re-do the cabin top anytime soon, and I prefer sailing to painting.
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You ultimately face the problem of differences in the coefficient of expansion of between different materials. It's why they don't use wood on new boats. You are doomed to repeat the process every few years. Rubber roof sheeting is fine for a roof but not a boat. You really wouldn't use asphalt shingles either. Primers with epoxy is about as good as you can do but you will still find cracks and require reapplication. Wood will expand and contract. Plywood has better dimensional stability than boards but it is something you have to maintain well or a little moisture and the whole thing expands from swelling and cracks the protective layer opening up more moisture damage. Epoxy has better UV / salt protection than rubber. Besides you really never want to be the ugliest boat in the harbor. Using a West System process would do about as good as you could expect from plywood. That is your best chance at a job that will last a lot longer than any other approach.