As far as taking waves over the stern, it was a concern of mine as well so I had the original battery box and livewell raised full height when the new transom went in with the idea of putting a "gate" forward of the engine but have yet to do so (when conditions are that sloppy in S. Florida, I simply do something else that day). So far, the new floor being nearly 3" higher than original has taken care of most water issues entirely. Anyhow, here are the redone stern area compartments - the base of the livewell is at floor level so it drains via gravity:
