It may not be gearing at all. Bearings can whine also, or cause gearing to whine. I would doublecheck your end play settings. Too much end play or too much preload - I'd suspect that they're too tight. What might explain the on and off situation is that the speed must be high enough to make the whine. We get that on our gearboxes at work - they won't develop any noise until the higher speeds (you should hear the whine at 30,000 rpm!)
Pinions should be set in preload (set by rolling torque - 8 in-lb max), gears (diff) are also preloaded, but set through a combination of case deflection and preload.
Check this out:
http://www.fnc.ch/Technik/9-Inch_rebuild.htm