Again, if you want to throw away $700, mail it to me. You need to do some due diligence and figure out what the issue is, rather than throwing parts at it. A clunk could be from a loose pinion gear caused by a bad bearing, or from issues in the carrier. You could also have loose u-bolts in the rear. There will be some noise from the axle wrapping from changing torque loads which is entirely normal in a truck.
First off, thanks for your advice!
Hah nice try, but I wouldn't spend the money unless I felt like it would solve the problem. Also, it's more of a sharp "ping" / "pop" metal noise. (definitely not a clunk) And I was born at night but not last night, so I can tell that this is not a normal noise caused by axle wrap. I mean, it happens at idle to 10% throttle.
I just got under the truck and placed my hand on the shaft while a friend caused it to happen (changing from D to R) and a ping can be felt. Definitely makes me still think it's internal/structural to the shaft itself. I've done some reading, on this and other forums, and found other guys describing the same problem. The dealer replaced the driveshaft and solved the problem. One hasn't heard it again, but the other had the problem come back after a few thousand miles; the main reason I don't want to go back stock if I do replace it.
I plan to take it off again sometime this week and feel the Universal joints another time. I know they all felt smooth and consistent the last time and the noise was just the same, and then go from there.