The clunk is my '09 Escape's drivetrain is finally resolved. The dealer I purchased my Escape from told me at two different recent service visits the noise was normal. The service manager verifyed the noise. I asked to escalate the matter, and the service advisor was to call me when a Ford Field Service Engineer was in town to look at it.
I still haven't received that call, but meanwhile, I took the Escape to a different dealer. Within a few hours they had the problem diagnosed as low transmission pressure and fluid. They then found the torque converter seal was leaking oil. Transmission fluid was down by 2 quarts. Apparently the leaking oil collects internally so there was no obvious external leak. They replaced the seal and fluid and the next day I picked up the car.
The noise is much lower now and shifts are solid again. The noise is still slightly there, but they say it's normal. If the noise would have been at this level all along I probably would never have even noticed it.
So, lesson learned about dealers. Needless to say I won't be returning to my original dealer for any service even though it's more convenient. I'm so happy this long ongoing problem is finally fixed.
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