Tough job, eh? When you are done getting the wood out, I would suggest using a wire wheel on the inside skin to rough it up prior to "peanut buttering" the new transom in. That will give the resin more surface to bind to. As well, I would suggest that you layout and drill out any penetrations that will occur in the new transom, about 1/2" oversize and fill those holes with peanut butter. That way when you install the new mounting bolts, transducer etc., the fasteners will not expose the wood to moisture. Also, I would suggest that you use resin to laminate the plywood layers of the new transom together rather than wood glue.
Looks good so far!