Shift boot
One thing that shocked me about my NV5600 transmission was the rubber shift boot. I took the floor console apart to add the Eaton/Fuller shift knob & vacuum plumbing so that I can add 2WD low and the exhaust brake enable/disable on the shift knob. When I get the console out I see the rubber boot is broken all the way around. Upon further inspection I find road grit on the shift mechanism and appears to have fallen into the transmission. I removed the shift tower and cleaned everything I could, drained the transmission, flushed the transmission (Yes $$$$), drained again, flushed, refilled. (I use the Mopar transmission oil for the NV5600).
A new boot isn't available from Dodge so I made one from a piece of motorcycle intertube. It is held on the transmission side by the shift tower bolts and on the shifter by carefully wrapping/winding around the shifter and then adding a large hose clamp.
Moral of this story - CHECK YOUR SHIFT BOOT! The road dirt ain't good for the transmission... .