Along with you, if it's only damaged in a small area, remove that area of damage, glass in the new wood, and be done with it. I say this for several reasons, one, you mentioned that you drilled stringers and transom "last Fall", and am assuming the core tests were good ( you didn't say there were bad ), second, if you only have a small area of rot, why would you want to bear the work/cost of replacing the entire transom, third, if it's a tiny area of wetness/rot ( may not even be rot ), I wouldn't worry about the engine falling off...LOL. Having said these things, if you do have a tiny area of wetness, there is a good chance that the water/moisture has "wicked" to other areas as well ( and from experience, it's basically impossible to dry out a transom ). And some years from now, if you really like the boat, have emotional attachment to it, you may want to replace the transom.