Turns out it was the rear end. When I took the diff cover off and checked the pinion I forgot to check the carrier bearings. According to the guy at J&P Standard Transmission my carrier bearings went bad, which killed the pinion bearings, which chewed up the gears and caused the whining noise. I'm not terribly suprised with how many hard miles the truck has on it. It was $670 out the door which isnt too bad especially considering they got it all done in a single day.