I say all of this normal. All my cars that are stout, hiss, scream, creak, clunk, bloop boop, and it means nothing. It's a heavy-duty driveline - it better clunk and feel solid. I've never owned supercar that didn't sound like it was breaking at low speeds. Lambos clunk endlessly, Z06 does 1-2-3-4 up, Ferrari does the clunk from 4 to 1 at all stops, and AWD rally cars sound like the whole drivetrain is going to explode shifting up and down...but they all don't break.
High performance cars /trucks (HD) are not the best DD. They make a ton of noise, and get crappy gas milage, because they're not made for DD. You can - I do - but it is the nature of the beast.
I suggest, some quit these neuroses, have faith in the warranty, drive it like you stole it, and enjoy it for what it is and isn't.