It sounds like you verified everything is good on the raw water side, except I'm not sure how you verified the mixing elbow isn't choked. I would take it off for inspection.
On the freshwater side, I would question/inspect the freshwater pump, the hoses, the thermostat and the exchanger. When I bought my boat, during the offseason, I pulled everything off that I was comfortable putting back together. I didn't mess around. I just replaced half a BOAT BUCK worth of parts, including all hoses & fuel lines, the 2 pumps, the thermostat, tested the injectors and replaced all the little bits that go inside the chambers. I pulled the heat exchanger completely apart and cleaned it thoroughly (even though it already looked really good). I looked into testing the fuel injection pump, but it looked good and testing it would have been the other half of the BOAT BUCK. It's worth taking good care of the exchanger ... that is a very expensive part.
My attitude when I bought the boat was that everything was 20 years old and I didn't have any history with it. When it's easy to replace parts and not so financially painful, I just go right at it. There is no sense in wondering how good are the old parts. A few of the really expensive parts that are obviously not suspect, I keep. But the water pumps and everything related, including sensers and whatnot - all new. That way, I won't be wondering again for 20 years, maintenance is straightforward, and I get to keep spares.
BTW, have you verified that you are actually overheating with a temperature gun? Perhaps the sensor is off?