The NV-5600's do seem to be rather "notchy" in the way they shift. Especially, in the lower gears (1st & 2nd).
If you haven't changed the gear oil, you might try that. Pennzoil makes a compatible gear oil that should satisfy your warranty, & it's cheap. The paart# is 3501 & I was able to find it at $4. 99/qt.
The last time I changed it, I used a boutique gear oil from a small company called Specialty Formulations (part # MTL-P). I did notice an improvement in shifting quality but, only a slight improvement. Some people, with other stick shift transmissions notice rather dramatic improvements. I believe that the NV-5600 is just so large & heavy-duty that nothing is going to allow it to shift like a BMW. This thing is a truck transmission and it shifts like a truck.
BTW, Red Line MTL has been used by some NV-5600 owners with good success. Again, you will probably not notice a big improvement, in my opinion.
While you are under the truck, you may want to consider installing a trans. filter, available from Geno's Garage. Just a thought.
Hope this helps.
Joe F. (Buffalo)