its probably the ring and pinion if they really replaced all the bearings that u say they replaced, if the preload and backlash are out of spec it will make noise, it can be corrected by adding shims to get the perfect gear mesh.
My question is instead of dumping all this money into this rear for parts and labor why dont you go to the junkyard and get a whole new rear axle, if its a 99 superduity the truck has a 10.25 full floater rear axle. they go for about 75 bucks at pretty much any junkyard and will bolt right in. make sure to get the same gear ration so u can use the 4 wheel drive withour grenading ur transfer case
- and im sure u kno but look for the (L) in the middle of the gear ratio for a limited slip, for example 3L55