Find it now, before you bolt anything new on. In order, I added to my 2009 GT: CAI and tune; shifter; Ford Performance handling pack (springs, struts, shocks, F&R sway bars, panhard bar); GT 500 front control arms; adjustable rear third link; adjustable rear control arms (poly + spherical bushings, per the late great Norm Peterson); spherical bushing for third link; one-piece DS; FP 4.10 and LSD. Somewhere along the way, probably after the handling pack, I developed a bad clunk in the rear suspension or driveline. After spending more time on my back than I want to remember and re-torquing every bolt 2-3 times, I couldn't find it. The shop I trust (who installed the third link bushing, new gears, and LSD after the clunk started) could not find it. It was not gear lash, but some jackass later told me it was and charged me several benjamins to "fix" it. Still clunks. I desperately want to track the car but I don't trust it. I have learned a very expensive lesson: Do NOT continue to bolt parts on in the hope they will fix the problem. Identify the problem first, then fix it. Maybe the fix will be a bolt-on like a one-piece driveshaft, maybe not.
BTW, please post if you figure it out. I'm still looking for mine. Thanks, and HTH.