Hi McFarm,, and welcome... I think your 80 series yanmar is a lot tougher than the 72 series I have.. At least from my prior reading over the years...
I think the idea of checking for bubbles in the radiator while it's running but still cold is a good idea.. I have read of those engines having a bad head gasket and also some reports of cracked heads..
Also, I removed my thermostat when I first started testing... I didn't think it was the problem,,, I just wanted it out of the way so I could check flow and bubbles and such without worrying about what the thermostat was doing or being in the way..
I hope you have good luck finding your problem ,, and please keep us posted....