I am having this problem as well on my 2010 Fusion Sport AWD. Took it to the dealer and they told me it was a bad torque converter. I figured they would be wrong, but I also had a different vibration about 60MPH so I let them fix that and it got rid of that one. I still have the one at 40MPH under light acceleration. They took my Fusion back yesterday and the technician said he thought it was driveline related and wanted to see what Ford would say to do, as they had never experienced this at the dealer before. (I wanted to tell them to come to this site, but I figured I'd let them call Ford first. )
So I will be checking back, but it appears I got a new transmission the first time (is the TC and transmission one piece?)
The service manager suggested i get a tranny fluid flush but I think that would be pointless w/ a new tranny. Also, they aligned it for me, because the "subframe had to be disassembled", which was kind of nice as I needed an alignment anyways, and it saved me $40. Now I will wait to see what I hear from them.