1996 rearend noise

You sound like you are well on your way to narrowing it down. Change out the transfer case fluid. In my book it says it uses Dex3 Trans fluid. You can substitute A full synthetic trans fluid meant to replace Dex3 if you want a quieter transfer case.

I always use a pure petrolium oil stabelizer (Only one that comes to mind right now is the Lucas product, but I'm sure others are out there) in my rear dif on higher mileage vehicles. It makes the gear oil stick to the gears better and fill in the little gaps left from wear and tear, making them quieter.

A whine can also be an indication of universal joints beginning to wear. If yours have a grease fitting, make sure to give them a little shot of grease too.