You should okay with the pinion depth since you're not changing the ring and pinion out, but yeah, I would agree that it seems the bearings may have been going and did some irregular wear on the ring which is causing the whining. A new nut is definitely recommended. It's a bit to swallow, but I'd get one at the dealer. That's one component (as well as the ring gear bolts) I would only trust with OEM parts. I don't have the specs for a 2500, but there are links to the service manual where you can check preload settings, backlash specs and the like. I would wager to say you already have some mileage on those "new" bearings so I wouldn't go by "new" bearing specs any more but perhaps a little on the high end of the "used" bearing specs.