When the clutch disc begins to fail, it can make a clicking sound that makes you feel its from the transmission..... if you have the beginning of clutch disc failure, you don't have a lot of time... .
We have several trucks with the NV5600, and have not had much problem with the transmission except for the truck we used to pull a 20K lb trailer... . what we learned was that the 6th gear was not designed for heavy pulling... this truck now has 300K miles... and is a intown truck... . no longer used for towing...
All the trucks that I've bought have the 4. 10 ratio so you really have to use 6th when you buzz down the highway with a trailer... .
If your on the west coast, we found a group of our customers in the CA, AZ, NV area with this transmission on the shelf... .
With this all said, we've started to upgrade to the 5500 and the new automatic, and love it... but it just has only 80K miles. . so the clock is still ticking...