If you seem to have an uncurable rear end problem, then maybe the problem isn't with the rear end at all. Wheel bearing drone can sure sound like a bad rear bearing. Try swerving back and forth at 55 mph and see if the noise gets better/worse as you swerve. If so, then you've got a wheel bearing problem.
Rear end problems will be consistent, get louder with vehicle speed, will not be rpm sensative, and may change volume with temperature of the rear end.
If you want to rebuild it right, I would suggest finding a speed shop that does Mustangs. The 03 Cobra had an IRS rear end in it, and in just about every young guys Mustang, they've changed the gears. That means that these Ford speed shops are going to be VERY familiar with setting up an 8.8 rear end.
Another great suggestions is to take it to a 4x4 performance shop. Those guys change gears really often too, so they should also be very good at it. The gears and bearings are available on Ebay cheap in both Ford Racing and Motive gears. Both are just fine. You can't change the gear ratio from stock though, without having your computer tuned for it. So don't go upgrading gear ratios without considering that.