Where can the FAA versus ICAO official filed differences be found? ICAO has a process where individual countries may file differences from the ICAO standard when the rules of the country do not coincide with the published standards.

Where can the list of differences that the FAA has filed be found?  I have found references saying that it is in the AIP, but I could not find a list in that document.

For instance, there is an ICAO requirement that certain aircraft are covered by a Flight Data Monitoring (FDM) program, but FAA rules say that it is an optional program and not required by 14 CFR.  

I found one (expired) document, paragraph 4b which refers to the FAA filing a difference with ICAO and want to see a complete list of all current differences.
The link you provide is for an amendment of the US AIP, not the entire document.

The entire document is available here: (link)

You will have to look at section GEN 1.7 (starts at PDF page 57).