So, what you are saying is that the holes have become oversized because you have removed and re-installed the engine several times. :noidea: OK, but just to be sure, check the holes for wetness and rot. If the wood is perfectly dry then try some epoxy to close up the holes a bit, then install the lag bolts.
If the wood is even slightly wet, then the epoxy will not work and you are more on the track that the previous posts have mentioned.
You could also drill a test hole on the side of the engine mount stringers, low near where it meets the hull, to see if you get water coming out.