The wood used in boat construction for stringers etc is not structural, it's merely a cheap form to lay fiberglass roving over to form a beam or stiffener. Often you see dimensional lumber like 2x10 used for this, as it is easy to work and doesn't require high levels of skill to cut it to shape. Cheap or poorly designed boats you will see these wood parts barely covered, not covered at all and just tabbed to the hull, or laid up so poorly that they rot and get waterlogged.
When you build the new engine mounts you might want to consider eliminating the wood to avoid possible problems. That is, you're going to encapsulate the wood, then turn around and poke 4 holes in there to put your lag bolts in. I would recommend a non wood core like HMMW plastic (King Starboard) Coosa, or even a poured thickened epoxy (use one for this purpose as layup epoxy will cook at a high temperature and ruin everything) into a mold made up from cardboard taped in place. You cover this with a few layers of heavy roving and you'll have good worry-free engine beds.
If you want to go the extra mile, set the engine in place, align it, then mark the holes for the mounts. Move the engine out again so that you can drill holes. You'll drill the holes 1/4 inch oversize, then using thickened epoxy, glue in 316 stainless steel threaded rod, as deep as it'll go.
