I pulled the U joint and I did not find anything obvious. The differential input shaft was tight with no play axially nor radially. The splines look good to me.
The drive axle splines also look good to me too.
The U joint was not loose and again nothing seemed out of the ordinary.
Differential input end.
Drive shaft end
Even the pins don't look bad. You can run a finger nail along their length and it does not catch and they feel smooth. They fit tighter on the on the shafts than on the U joint but it is not a "press fit" on either.
Normal wear and tear? Tolerance build up? Reassemble with some grease to reduce the perceived knocking? Replace the U joint and/or pins?
These mysteries to be revealed on the next episode of "As the Kubota axle turns" ...