Connect the garden hose...
 

and pull all the spark plugs out. Crank the engine and see if water squirts out of the spark plug holes. If all the cylinders stay dry, it HAS to be the exhaust headers.

There really is no other way salt water can get to the cylinders.

How is it running? Did you do a compression or leak test yet? A low or dead cylinder will draw water in.

fresh rebuild 20 hours compression good thru out.

Does it have lengths of rubber hose between the headers and the transom? I have seen one of these break inside and act like a flap, made the water revert right back into the engine.

no