97' 3rd gen here. I kept blowing rear pinion seals and had my bearings replaced in the diff. I was told by Toyota mechanic it was a bad pinion bearing.
After the bearings replacement, I had a very audible whine upon decel at basically highway speeds. On every single decel, it sounded like someone punched my rear 3rd in the stomach and she was crying.
I took it back to the mechanic and we took a quick test drive. Within just a few minutes, we turned around and he said he didn't set the backlash properly on the pinion/or other bearings (Don't remember). He tore it all apart again under warranty and reset the backlash properly. Very little/to no whine since.
My point is -- your initial thought of a problem with the pinion bearing is very likely correct. It may be the backlash though and not the bearing itself. This is a relatively complex area mechanically, I honestly had never heard of a bearing backlash 'setting' before my incident.
It really sucks you didn't get new bearings in the rear diff when you just had her cracked open for the elocker.
Even if it's just the backlash and not the bearing, if you are going to in there a 2nd time, I would buy a bearing set from Yukon or ECGS.