A friend of mine had this problem with his IO. What we finely found was water getting into the cylinders through the exhaust. It didn't happen all the time. We ran it with out the water cooled manifolds and just a set of headers. It ran just like it should. put the water cooled manifolds back on and back to the problem. there was a rubber flap at the rear of the boat at the exhaust exit that was bad. I'm not saying that's your problem BUT. I know first hand there is not a lot of room to work on these. In the beginning we took the engine out thinking it had a cracked block. We fought it for two boating seasons. It runs fine now. Good luck