UPDATE
Last time I had put it all back together and built a small engine stand to attempt starting it while separated from any possible "downstream" source of resistance based on the recommendation of the guy at the machine shop. They had rechecked all clearances after I had torn it back down after the initial attempt to run it after the overhaul. Initially it would run maybe 20 seconds to 30 seconds before appearing to get hot and stop running. After putting it all back together and in the process getting the timing gears aligned correctly (think I had crank shaft off one cog when I put it together the first time) it ran for what seemed liked a few minutes (did not time) before it appeared to get hot and die. Thinking I had it right this time, I put the engine back on the tractor and checked the injection timing. The injection pump was set up like it came to me, but appeared to be off 5 degrees. I adjusted the shims until it appears to be right on based on the very first indication of injection at 25 degrees BTDC on the front cylinder. I had also noticed it was missing the fan shroud, so I bought one of those and installed it along with a temp gauge in the upper radiator hose this morning.
My neighbor has the same tractor, so I had him run his at idle for 3 minutes so I could see how hot his appeared to be getting and how the heat was moving across the radiator. After running for three minutes, the head was pretty hot but I could put a finger on it briefly without too much discomfort. The radiator was hot at the top only, similar to what I have observed on mine.
This morning, I was finally ready to try it again. Bleed the fuel lines, filled the radiator and fired it up. It idled very smoothly, with no smoke. There was just a little smoke when I would accelerate, which is normal per the manual. It ran fine for two minutes and began to show a hint of smoke and then died. I was showing about 45 psi oil pressure the entire time and the temp gauge only got to ~120 degrees. I had left the radiator cap off and no bubbles or any other unusual observations. The head was hot, such that I could not hold a finger on it. Not scientific, but did seem to be hotter than my neighbors tractor after his ran for three minutes. I looked everything over, started it up and it ran for about one and a half minutes and then appeared to bog down and die.
I am really at a loss, as it seems to be running perfectly but then appears to get hot and try to seize up. It never has boiled over and the temp gauge never got above 140 degrees, although head seemed hotter than that to the touch. I am wondering if it could be running too lean and getting hot??? I have not checked the injection pump but the tractor has about 2600 hours, so I guess it could be worn and causing a lean condition. Anyone have any experience with this??