Check the pinon nut - but you'll have to drop the rear d-shaft to get to it. Don't wait on this - very bad things happen if the pinon nut backs off all the way. Not sure why the noise would have been affected by your pulling the d-shaft, but who knows.
Steve H. - KE0KNH
Colo Springs, CO
'78 FJ40, '89 FJ62, '98 4Runner