[willy]

Shifting the weightof a battery forward and especially if you are going to add another I would recommend.
Sean I had a real nice CC Robalo that had the exact problem you are having, was not cut as low as your notch but had less buoyancy and max HP (heavy engine) and every bob up and down put water splashing onto the floor. It would drain out but not the best set up.
Consider
1. shifting weight forward
2. installing a lighter weight motor
3. redoing the transom, either as a 25" notch
or better yet
4. Close the notch and install a bracket

JMHO been there and done that and won't ever again ;)