Sorry for the updates, but I have been very busy with work and traveling often so there has not been a lot of time to work on the Kubota. Since I got the engine running a few weeks ago I have put about 10 hours on the rebuild. Unfortunately, it has developed a tapping sound that is loud enough for me to be concerned. What is odd is that the tapping is not always present and will randomly go away for no apparent reason. I have tried to pinpoint when exactly it will occur, but have been unable to create a scenario where I can replicate it 100% of the time. It seems to be more noticeable when the engine is cold, but there are also times when I don't hear it at all after a cold start. The tapping will subside as the engine is revved, but it is definitely still there and may just be drowned out by the increased sound level of the engine at higher revs.
I was so concerned with it that I drained the oil (again) and dropped the oil pan and inspected the brand new rod bearings, but they all looked as good as the day I installed them. I also suspected that the valve clearances were out of spec (and they were) so I adjusted those to the factory manual, but the issue did not improve.
At this point I'm thinking the tapping may be piston slap on the #3 cylinder, which is the one I had to bore out to remove the marks left by the previous piston and its seized wrist pin bearing. My belief is that I removed too much material and the new piston/rings fit a lot looser in the cylinder bore and the piston skirt is tapping against the walls and creating the noise. I did measure the cylinder bore after my honing process and it was within factory spec, but it was on the higher side.
My plan is to just keep running the machine until it dies. It may last only 25 more hours or it may keep going for another 2500. Who knows. If the engine grenades itself, I'll find another one to throw in. Once I get this to my parents farm I'll have a lot more flexibility when it comes to major repairs like an engine swap.