When I hear someone complain about “knocking”.... I think about mechanical failure of main or conn-rod bearings or piston-slap due to mechanical failure. (Diesels have a ”light knocking” sound which is quite ordinary because of the compression-ignition system. A true “knock” would be caused by mechanical failure.)
A stethoscope might isolate the location of the ”knock”. If it is coming from all cylinders you might consider having a professional diesel engine technician advise you further.
Otherwise, I’d drain the oil for spectroanalysis and cut the filter open to look for metal, and while the drain plug is out, use a boroscope to observe the condition of main journals and connecting-rods at the cranshaft while the engine is slowly rotated forward and backward looking for contrary movement of the conn rods at their bearings with the crank. Look also for camshaft looseneess (might require removal of a gearcase cover.)
A Kubota dealer with an experienced diesel technician can be your friend here.