Do you have aftermarket poly lcas? maybe greasing time. The rear sway bar end links are notorious on these cars but, they usually create clunking. Ford will generally replace them with better ones under warranty without too much fuss, or you can cure the problem yourself for as little as 25 bucks by replacing the rubber with poly bushings from Energy Suspension. Ol' torchy gets the bushings out pretty quick.
2014 Premium GT, SGM, Brembo, Auto, Tech, Comfort, etc. GT500s, Steeda UCA, VMP auto N/A tune. 100 shot nitrous on BBR tune. Best e/t 11.38 at 120.85
2012 Premium GT, Candy Red, Brembo package, 3.73, MT82, Comfort, Tech, et al. Procal tune, Roush UCA, UMI poly LCA, GT500s, Steeda red bracket, Hoosier 28x10x16 bias drags. Best e/t 11.91 at 115.23 RIP