Rearend Noise - 8.8, Please help

I am hearing a mechanical noise coming from the rearend on my 2000 Mustang GT. It seems to be based on rotation of the wheels but I cant tell exactly where it is coming from due to the exhaust. I have lifted the car and let the wheels spin at different speeds to determine what is causing the noise but the exhaust drones out the noise when I am under there to determine exactly where it is coming from.

I recently had to change out an axle due to a wreck. I bent the axle and so I replaced the axle and pack bearing that is located within the axle tube at the hub. I did not replace the axle bearing. I filled the rear backup with the correct oil but forgot to add the Friction Modifier. I drove this for several thousand miles before figuring out I needed to add the friction modifier. I have just added the friction modifier but that did not eliminate the noise.

Can anyone help me determine what this noise is? I am not sure if it is the axle bearing or maybe the ring and pinion is making this noise.

When you say clean everything, what do you mean? I understand there might be small metal flakes or trash or something in the rear but how do you clean the rears? Is there a certain chemical to flush the system out with and then add oil? Example, brake cleaner fluid then let dry and add oil? Appreciate the help.