If it comes from the rear its the gears. Improperly installed or just wearing over time will give you the infamous "mustang clunk". Could also be a UCA or LCA bushing, broken spring, all sorts of stuff that can be bad. Check your u joints too.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.