JammedStab,
From my experience that noise you're hearing in the flightdeck and on the maindeck below could be a dried out nose gear steering collar "groaning" during turns. Engineers tell me they usually give the collar a good lube and problem noise disappears. Also, one would think that sitting in the flightdeck with engines running, you would be too far away from the body gears to hear any noise emanating from them unless maybe a severe structural failure that I would guess you would feel through the airframe as well.