Your symptom description sounds too similar to my experience to not mention. My symptoms were acceleration going flat at the top of the gear. There was carryover into the next gear. Before going into the dealership, I also noticed a sound coinciding with the performance flattening that sounded like a belt squeal. The dealership duplicated the symptoms and claimed that the car thew a code for them. They explained that (their words) I had a vacuum leak at the high pressure fuel pump sensor, which caused an over boost condition. I'm thinking that the car pulled timing to protect itself. They told me that Ford did not use a clamp on the site of my leak. What they did was to trim the hose and add a clamp. Problem has not reoccurred and the car pulls strong to the top of gear and seems to leap as it hits the next gear. In normal driving I was unaware of the slowly developing issue. This may not be related to your problem but I could not help but see a similarity in your description of symptoms. Good luck finding your problem!
2010 Steel Blue Metallic, Fully Loaded, non PP, LMS 4+, K&N drop in, 170 T-stat, 3 bar MAP