Those are going to sit below the water line which is fine with the snails you're running. My Miller was set-up real similar to your boat. You can clearly see in the pic those ugly flappers don't seal even when new, they aren't supposed to/don't need to seal completely. Flappers just slow the water flow down. Through transom headers aren't going to solve anything other than emptying your wallet, unless there is a problem with your logs and/or snails.
I remember reading somewhere that you pressure tested the engine, was that including the logs and snails?
Something ain't right in here...