Jony There should not be water in the exhaust port, if there is water in the exhaust port, then there could be water in that cylinder and that is a No No. The water cooler exhaust should be a sealed unit and operate with the the raw water cooling system. Because it is a raw water cooled engine, ie sea water, corrosion is a major cause of any water leaks.
Did you have the head checked while it was off the engine. You may need to remove the head and complete detailed inspection. Have you checked any sacrificial anodes in the engine. Bob