It sounds like we have a similar arrangement... (obviously vastly different boats). My engine and engine room are accessible via the cockpit sole plate. Once I open that, I am into the heart of the boat, right down to the depths of the bilge.

I recently replaced the seal on that sole plate, but it occurs to me that if I were boarded by a major wave, and water found it's way down through that seal... not a good thing.

How is your cockpit sole plate sealed?