Originally Posted by joes06tacoma
If the noise goes away when you press on the clutch lightly, it's the TOB. If it only stops when the clutch is actually pushed all the way down, it's the bearings/gears in the transmission. If it's the transmission, you've likely got some time before it's going to actually go out. Our 04 2wd 2.4 5 speed at work has been doing this for the last 50K miles.
now I am only trying to help, ok, I have never had a transmission, or gears bad on me, but this goes back to the mustang, and this was just white trash... .but a year later, the transmission started leaking oil, it needed a new main seal, so I had to save up, was going to let a garage do it, and it took a few months, so every 2-3 weeks I had to stop in a garage and have them refill the transmission, and I would know it was low when it started to moan, and it was in the first two gears, but this was a different deeper sound and if you listen the throwout bearing is forward, and the transmission noise would come up beside the driver. since i have been under mine a lot, is should be the same...listen to see if the sound is coming up by the stick, that is where the noise was on the F350... hope is some help.