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 build #48. Bolt ons, suspension, Novi 2000.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.