If your engine is running too hot there will be one of two reasons. Either the water pump is not moving enough water, or the water passeges have become clogged.
So, check your water flow, but you say you have enough. So the next thing to do is run a mild solution of muriatic acid though the outboard. This will clear the internal buildup of crud.
You can purchase muriatic acid at any swimming pool shop or any marine store that deals with Lectrasan toilet systems.
That should solve the heating problem.
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