^^Yes. The symptoms actually sound more like poor cooling air or water (or both) flow. This could be due to radiator/thermostat/water pump problems and not the head gasket. Or even just a loose fan/water pump belt! Since it is disassembled to this degree now, would probably be wise to pull out the radiator for a thorough inside and outside cleaning. If you can still find a "radiator shop" in your area! The thermostat may have been hanging partly closed. A replacement thermostat is cheap and good insurance. There's a chance that the water pump impeller is degraded just due to age or poor cooling system maintenance. This can usually be verified just by pulling the water pump and only the cost of a new gasket is involved if it is ok.
So the previous overheating MAY have not been severe enough to warp the head. I have no idea how prone 2-cyl Yanmar heads are to warpage. Some heads are really tough, others not so much. But since it's off anyway, no good reason NOT to have it checked and resurfaced if necessary.
If a machine shop doesn't have tooling to remove diesel injectors, you definitely DON'T want to use that machine shop!
I will pull the radiator and water pump and see how things look. And also look at the air filter and hoses to make sure we are getting all the air we need too. I will do some digging and see if there is a good shop to take a look at the head and radiator if possible. At some point I have to put a battery in the tractor to do some wiring/electrical trouble shooting to make sure everything is working right. Thanks for all your help!