UPDATE
My new infrared temp gauge finally arrived so I was able to actually measure the temperature after running the tractor. Started it up and it ran for right at 2 minutes before bogging down and dying while emitting a small amount of black smoke. I took measurements of the top of the head:
front 156 F
middle 170 F
back 156 F.
I started it again and it ran for about one minute and 20 seconds before dying again. I tried to keep it running by speeding up the motor and it did briefly speed up before dying with even more black smoke. I does not appear to be starving for fuel. After this run, the temps were as follows:
front 161
middle 186
back 173.
The radiator core showed 157 near the top. It does not really appear to be overheating and I am going back to the machine shop recommendation to looks "down stream."
While running the tractor, I moved the three point hitch lever for the first time that I can recall every giving it a try. The hitch raised up just fine, would stop and hold (based on hand pressure) and would lower back down under hand pressure. When engaging to lift, there was a slight sound of gears meshing. I ran it to the top, moved position lever to neutral, and tried to move the lever to the up position again and heard a definite sound of gearing trying to mesh but could not get it to "engage." I did not force it, as it obviously did not want to engage under these conditions. Is this normal behavior or should it allow you to move the lever into the lift position and allow pressure to bleed off since the lever is already up???
I still need to recheck the injection timing, as I don't think I had the fuel lever all the way to wide open throttle when I last checked it and adjusted the shims. I have not used any sealer on the shims. I cannot now remember exactly how many are in place and they differ thickness anyway. I still have the original stack that came out ready to go back in based on checking again with WOT.
After the last assembly, I did run the motor on an engine stand before mating it back up to the transmission. Unfortunately, I did not have my timer running but it certainly seemed like it ran for longer than the two minutes max that I get with it on the tractor. It did die, as now, but I do not recall if it had any black smoke?