You should also blow out your radiator if you have not already done do. I'm not familiar with them (Yanmar) but my old Kubota tractor basically had a wimpy radiator. It has a screen on the intake side that needs to be cleaned regularly or it will overheat, even with fresh coolant. I clean the screen after every use and blow the radiator out regularly depending on conditions. The tractor is about 40 years old and still runs pretty good. I think the radiator is undersized although if clean it works just fine.
Once you checked all that I suspect you might want to look into the thermostat and/or the water pump.
