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I had the same experience with my Westerbeke 30. I opened the heat exchanger and confirmed that all the little tubes were free of debris, yet the engine was still running hot.
The problem turned out to be caused by a chunk of the exchanger zinc that had broken off and found its way into the 90 degree elbow fitting that is the outlet of the exchanger. Other little bits of stuff settled in around this larger chunk and all but clogged it right up. This was not immediately visible when checking the cooling tubes. Hope this helps.