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First of all I don't think its really catastrophic that your engine mounting bolts may have been made a little too tight and now you have dents. We're it my boat I would get one of those aluminum or stainless steel plates that spread the load and use plenty of bedding compound in the holes and under the washers / spacers / plate. As far as the core of the transom goes, if it's wet then water is getting in there somehow. In any case if you're putting the boat away for the winter, can you remove the engine and leave the holes open to dry out? Maybe put the boat in your garage to keep out water. Oh, the wood you are sticking the pick into inside the hole is end grain plywood so unless you can scrape out rotten wood I don't think you have a rot problem. There are a lot if people on here who know an awful lot about boats so I hope if I've misstated something someone will correct it.