What I didn't see (missed it maybe) is mention of the
raw water injection into the exhaust. Usually there is a pipe from the
cooling water to the exhaust
elbow. When the engine is off, depending on the height of the
cooling elbow and the outside water level, raw water in the
heat exchanger can flow through the cooling system and into the exhaust pipe (it siphons actually) and if it fills the exhaust pipe, and then fills the exhaust manifold then it can flow back into the area of the
head where the exhaust valves are. If one valve is open water will fill that cylinder.
To check this you only need to un-do the raw water injection hose from the elbow and move the end up or down to see whether and at what point cooling water runs out the disconnected hose. Keep in mind that the exhaust elbow may have an extension to the cooling water tube inside of it, effectively making the end of the hose a couple inches lower than where it connects.
Even if the engine is above the exterior water level the raw water in the
heat exchanger and other
parts of the system can siphon to a lower level through the raw water injection hose into the exhaust and if that level is above the exhaust valves...trouble.
The solution is to put a siphon break in the raw water outlet before it enters the exhaust elbow. I run the water hose up to a
cockpit drain and put a small ball valve there which, when open, allows a small amount of cooling water to go into the
cockpit drain, (which I can
monitor by looking down into the drain) and then the hose goes back down to the exhaust elbow. Some people put that opening into a
galley or
head sink. When the engine is off air flows back into the hose breaking the siphon.
This
solved the problem I had with water getting into the cylinders.