I don't think these older (70's) Japanese tractors were intended to run as hot as a modern diesel where clean exhaust is a concern.
User manuals in English for the US versions seem to consider some owners will drain the radiator when the tractor won't be used for a while, then fill up with rice paddy water + water pump/antirust additive when planting season returns next year. The manuals also discuss running without a battery. Apparently the design anticipates that some owners will jump the tractor every morning to get it started in the few days a year that a rice paddy tractor is needed.
This is simple bulletproof technology - a diesel water buffalo, to exaggerate a little. And that light use/simple design is how importing 40 year old used tractors makes sense. Not worn out, and simple to maintain. (YM3000 = YM2000/YM240 with one more cylinder and a heavier chassis).
The fishing boat versions of these same engines - 2Q, 3Q etc, run full power for hours/days without problems. That's much harder use than the intermittent loads on a farm tractor, and reliability is more critical considering changeable weather on the open ocean. Those are considered unbreakable.
I think this YM3000 cooling system needs to be brought back to spec by rodding or replacing the radiator. Then it should be good for a few more decades.