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I'm currenty doing what I can to dry the holes enought to temporarily fill them so I can use the boat through this season and address the transom over the fall/winter/spring. There's no flex to the transom
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If there's no flex, there is no problem yet. It's not like cancer, the worst thing that will happen is you'll eventually need a new transom, but that could be ten years away or longer(I recently sold a boat that I had for 13 years. The transom bottom always seemed wet, yet it was solid where the motor was mounted).
I would unscrew everything currently screwed into the transom and let it drain for a while. It can be helped by using a wet vac over the holes. After a few days or longer, use a bent nail in a drill to pulverize the wet wood behind the screw holes. Use your vac to get it out. Then fill with epoxy and cabosil. When dry, refasten your fixtures by screwing into the solid epoxy. Use 5200 on the screws.
FWIW, saltwater does not rot wood, though it will soften submerged plywood eventually. The difference is that if you dry out the wood a bit, you may have no further damage.