I just read through your entire thread for the first time. My first thought was that the starter was staying engaged and dragging down the motor. But since you can start it every time and haven't had trouble, I quickly ruled that out. My second thought, and now my leading concern, is the hydraulics. You say there is no backpressure, but I am still skeptical. Have you tried running the engine with the hydraulic pump disconnected? I would suggest disconnecting the hydraulic pump from the engine. Make a simple falt plate to bolt in place to keep dirt out and the oil in. The bearing is only under splash lubrication, so no excessive oil pressure to worry about. With the hydraulic pump disconnected, it can definitely ruled out the hydraulics as a problem, or definitely point to the hydraulics as the source of the problem.
I work on Kubota diesels a lot, and on a few occasions have test ran an engine with a seizing hydraulic pump. It definitely puts the engine under load, and make a bad sound while doing so.
Thanks for the suggestions. In these cases, was the seizing occurring the entire time you were running the motor? Mine is just fine for awhile and then suddenly comes under load. After waiting about 30 seconds, then no load on the motor.
After I put the motor back together for the second time, I built the makeshift engine stand and ran the motor without it hooked up to trans or hydraulics (pump on motor, but lines not attached). This was awhile ago now and I cannot remember for certain if I shut off the motor or if it eventually died on its own. I do know it ran for a while and much longer than it was running before. At the time, I was not sure why the improvement as I did remove a slight bit more from the rings to increase end-gap. I don't think it was the change in the end-gap but thought it more likely related to something connected to the motor (hydraulics or trans.). The guy at the machine shop, who has a lot of experience also thought it more likely it was some other than the engine causing the load.
I checked the pressure on the hydraulic line running from the pump to the connection beneath the seat. There was essentially zero pressure as the motor ran and would get a slight bump as I raised the three-point lift. At the top of the lift, the pressure would spike and then the lift lever would be returned to the neutral position at which point the pressure went back to zero. I do not hear any noise or otherwise signs of problems with the pump. During all of this time, I could usually get the motor to idle for up to 5 minutes before bogging down and dying.
I shifted my focus to the transmission and at first when I tried to drive the tractor, I had the same symptom (idle for 5 min and die, or run shorter time if higher rpms). I have kept at this every weekend or two for the past couple of months. I would just do it for a short time and put it back in the barn. A few weeks ago, I decided I would just keep at it until one of us gave up. That day, the tractor did not die on the first attempt, I just kept driving around the yard (at idle in low range) and then let it sit at idle for probably 30 minutes total. If I went much faster, then it would die. Now, a couple of weeks later and after several more runs of 30+ minutes, it will run indefinitely at a fast idle, I would guess may 1,000+ rpm. Another change that I have noticed is that it does not die as quickly and seems to bog down with less restriction. Yesterday, for the first time I was actually able to keep it running by slowing it back down to idle when it tried to die after running at faster speed. Before, it did not matter, once it started to die (bog down), you could not do anything to stop it from dying.
This improvement after driving it around, made me think that somehow it was related to the trans, as I believe the tractor sit for sometime before I bought it and rebuilt the motor. However, as Kutobasam noted above pressing in the clutch does not appear to have any impact.
I will take at look at hydraulic pump to see if I can separate it from the motor while keeping the lines attached. Otherwise, as I seem to recall from past attempts along this line it still pumps hydraulic fluid out of the lines; I guess pressure from the trans???