I have a Yanmar 3gmd (30 years old). Runs good except even in neutral I only get to 2700 rpm (based on yanmar tach). In gear and moving at 6.5 knot hull speed the rpm is also 2700. Engine has all new filters and exhaust elbow is good. Exhaust color is normal. Not sure what my problem is either. One thing I have noticed is that when the engine is running I do not have fuel being returned via the fuel return line. I need to look into this more. I am thinking my fuel injection pump is not putting out enough fuel. The lift pump on my engine is new.
One thing is the bleed screw on the top of the Yanmar fuel filter housing has a plastic gasket that can crack and let air in. You may want to replace.
Let me know what you find.