According to ABC News, "A photo shoot involving a 747 used as Air Force One and one fighter jet flying at low altitude led to hundreds of frightened calls from residents and workers in Lower Manhattan this morning, triggering memories of 9-11 as many evacuated their offices. The president was not aboard."
I immediately submitted a FOIA request for all documents relating to this flyover, including electronic communications etc. To my surprise, I received not only all communications, approximately 1,000 pages, but also all of the photographs taken that day as well. Below, you will find all of the .pdf files that were obtained via CD-ROM. I split the 350mb files into multiple parts for easier downloading.
The Flight Manifest for the Flyover [1 Pages, 430kb]
Electronic Communications, Part 1 [199 Pages, 55.1mb]
Electronic Communications, Part 2 [200 Pages, 83.7mb]
Electronic Communications, Part 3 [200 Pages, 82.6mb]
Electronic Communications, Part 4 [299 Pages, 55.9mb]
Electronic Communications, Part 5 [191 Pages, 151mb]
The Photographs [147 Photos, 6.4mb]