Overfilling the reservoir, huh? Might want to do a combustion gas test. I swear that soot thing is not that unusual, but yours does seem excessive. I'd try to figure out the source of the oil into the turbo (crankcase, air compressor, or the turbo itself) and address it. Have the exhaust brake setting checked. A crankcase breather filter can be added, you need filter and the cap off of an 11-up Hino conventional. it sticks up about 2" higher, make sure there's clearance when lowering your cab.
On the Hinos, if it's doing a driving regen and you stop moving, you'll have a warning pop up saying that a regen is occuring. That just means not to park in tall grass, not that a manual regen is required. Start moving again and that warning should disappear. I don't know the specific behavior of the Hino-powered UDs, whether or not the exact things happen.
Any software updates will have to happen at UD.
Improved injectors with enhanced antiwear coatings inside them were not offered to UD. Hino injectors can be installed, but the cal codes cannot be entered. They seem to run just fine regardless. The unimproved injectors were pretty crappy. Do yo hear it nailing when it's cold/hot/undervarying loads? Does it ever roll coal?