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Hello. My name is Tan.
I would start with a compression test. Blow all the water out of that cylinder before you do the compression test. If compression checks good start the engine. Let run for a few minutes at about 1200 rpms. Now shut engine off do you have water in any of the cylinders?
Diod you over heat the engine?
Is this boat used in salt water?
How many hours are on the engine?
Yes manifold or riser. But with low hours it's hard to say and especially freshwater.
A sticking valve will allow the cylinder to suck water into the engine. This is the purpose of the compression test.
Did you have a following sea when in rough water?
Ok if compression checks good put plugs back in and run engine for about 5 minutes at 1200 rpms. Then check for water in the cylinders. If you have water then we need to remove the manifold and riser and inspect. If no water it is possible it came in through the exhaust when you were in rough water.
Ok the compression test is going to tell us what happening. If you have a stuck exhaust valve it will suck water into the cylinder. The piston going down creates a vacuum.
Was the spark plug rusty?
Ok at this point we need to do a compression test and go from there.
Keep me posted... Thank you...Tan