Did anyone find a resolution to the clunking sound? I have the same problem on my 2009 Limited NA. I've replaced struts, strut mounts, sway bar end links, sway bar bushings, inner & outer tie rods, rotors, brake pads, new tires and the clunk sound is still there. All replacement parts are Ford genuine parts. The only thing left to replace is the lower control arms but they were replaced 5 years ago. I seriously spend more time working on it than I get to drive it. The creaking sound that the OP mentioned is the upper strut mount. I had the same sound like a spring on a old wooden screen door. All I can say is that if you don't use genuine Ford parts you'll be forever replacing parts on the Flex. I guess my last hope is to replace the LCA's again and if that doesn't solve the problem I'll be selling the Flex.
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