Mike,
I believe that engine is thermosyphon cooled (no water pump) so there should be no agitation in the radiator. If you're seeing movement, I'm guessing it's from air bubbles making their way through the cooling system. What appears to be a water pump is actually what Kubota refers to as a "dynamo" and is actually the alternator for the charging system. You can be sure of this by locating the charging wires that come out of it behind the fan pulley. No water pump would have a charging circuit built into it.
You can go to the kubota.com site > parts tab > illustrated parts list > accept the agreement > and input B6100 into the search box. From there choose "Open" for the "E" model. Then on the left side of the box that opens, choose "Engine" > "Dynamo group" you'll see what I'm talking about.
I would suggest pulling the head to see what you find. If you get lucky, it might just be a blown head gasket. Unfortunately, the thermosyphon engines tend to overheat if folks don't keep the radiator clean. Often it would result in the head cracking. No way to tell until you take it apart, but I'm suspicious because you mention also having white smoke/moisture in the valve cover area.
You will be able to tell which cylinder is burning the water because it will be very clean.
Regarding the injection pump leaks, I don't believe it would cause the issues you're experiencing. Yes I'd replace the o-rings and crush washers, but based on your spray pattern test, I doubt the leaks are enough to cause the knock. It would have to be leaking to the point of significantly dropping the pressure to the injector for it to potentially cause a knock (and then I don't even know for sure if it would). If that were happening, you'd have diesel spraying from the pump area and going everywhere. It doesn't look to me like that is the case.
Finally, yes it looks like you might be in for a rebuild. You may just be able to replace the head gasket and go, but I'd take the head to a machine shop while its off and have it pressure tested and checked for cracks. Depending on how many hours are on it, might be worth having a valve job and surface done at the same time.
Then you get into the balancing act of deciding whether or not to go through it while you're at it or just fix what you find. That's your call to make. I can tell you that D750 engines tend to go through eBay for about $1000 - $1200 so that will give you an idea of potentially what you're in for.
Finally, grainfarmer has new and used heads for your engine. (no I'm not affiliated with him in any way) If your head is bad, you may just be able to slap a replacement on it and go.
http://www.grainfarmer.com/kubota-engines.html
It's hard to know the best option because we don't know how much blow-by the engine has. Hence, it would be a bit of a gamble on your part. That being said, if the engine is not worn out it could very easily be just fine. Worst case, you end up tightening up the top end and figuring out the bottom end is too worn and you end up going through the bottom end later. If it's anticipated at the beginning then any potential curve-balls would easier to deal with. Yeah you waste a head gasket and some time, but the work done to the cylinder head would not be wasted. The only other curve-ball is if it would have been cheaper to just replace the whole engine instead from one of the eBay importers. That would also give you the advantage of being able to up the horsepower while you're at it.
It's a cool little tractor and will be very handy once fixed.
Sorry for the bad news. I hope I'm wrong!
Steve
