I don't have enough experience to even guess at the noise, but from what you say about shifting would it make sense to drain the transmission, unhook the shifter links and pull the side case to look inside? At least you're not removing too much right away. Another thought is to raise the truck and run the engine and driveline to listen for the noise. But do it safely. Maybe you know of a shop that can put it on a chassis lift for you.
I just have to shamelessly gloat .
Gave you this guess back in 2010. Glad it worked out just fine.
