2009 F150 STX 4.6 v3 with 6 speed tranny. Have same clunk issue. When slowing down and then give it some gas, feels like bottom dropping out of truck. It is much worse when towing say uphill hard and it has to down shift. It's not the first downshift but the second. Took it to the dealer and they reprogrammed it. It is not gone, but happens a lot less.