I have the same exact problem as you. I'm thinking about putting back my stock rear springs to see if that fixes the problem. You're right when you say it's hard to enjoy your car when you hear all this clunking in the back.
Don't waste your time with the springs, I already tried that. I think it might be my sway bar or maybe my panhard bar.
2012 mustang v6 performance package, power mods: airraid intake, borla s-type exhaust, appearance mods: saleen front grille, hood spears, roush side spliters, 2013 tail lights, retro fitted head lights with led and hid, shorty antena, black deck lid, gt500 steering wheel, oem take off leather seats, retro black shift knob, suspension mods: koni shocks/struts, sr springs, gt500 top mounts, panhard bar, lca.
1994 mustang gt 5.0