Just replaced the timing chain on my 5.9, but i dont know much about timing chains in general, my old one was fine but i replaced it cause i was fixing the gasket leak i was having. Anyway, i heared if your chain is bad it can cause problems with starting and grinding noises in the engine.
Have you had someone actually put it in park/reverse ect while you were up front listening ? I ask this because it could possibly be the transfercase or transmission doing this.
Here is a writeup i found on replacing the I6 timing chain