It is almost guaranteed that one of your suspension components is not tight enough. Go through every threaded fastener of your rear suspension and check it for proper torque. You will find it. Shocks bolts are the most likely problem area but it could be any component. I had a thump in my rear end and it was the adjustment sleeve of the adjustable panhard bar.
2012 Mustang GT, Brembo Pkg, Yellow Blaze Metallic