You might want to try disconnecting the speedometer cable at the transmission and see if the noise changes. It may be the little gear set for the speedometer, stranger things have happened.
Also, check for water in the transmission. I have found water in mine even with no apparent source, just from sitting and condensation. It doesn't seem to have caused much damage but I've gotten into the habit of checking it after the truck has set for more than a month. That was when I kept it outside, though. My garage I keep it in now is pretty well temperature controlled.
