Pulled the truck out of the garage and did some testing. I put the transfer case in neutral so that I could run the transmission into the gears without any road noise. What I thought was only happening in gears 1-3 is actually happening in all gears. Its a somewhat big rattling noise that happens any time the clutch is engaged, and in any gear. When I disengage the clutch, the noise goes away. I put some pressure on the clutch pedal to get some pressure onto the throwout bearing, but that didn't make a difference.

I think that all this points to the input bearing, which it's my understanding can be replaced without tearing the whole transmission apart, is that correct?