How much jurisdiction does the FAA have over military aircraft?
If they are being operated by the military, not much. Military operations can exempt themselves from the FARs (as a matter of practice they don't: When operating in the US National Airspace System they follow the same operational regulations we do, but as a matter of regulation they're subject to the military's rules for airworthiness, maintenance, etc.).  

Military pilots have a military pilot's license (which can be converted to an FAA license with a little paperwork), and the airworthiness and maintenance standards for active military aircraft are defined and managed by the branch of the service responsible for the aircraft. (This is similar to, but legislatively distinct from, Public Aircraft Operations.)

This doesn't mean the FAA is completely silent about military operations/aircraft: There is guidance for military aircraft that are based on commercial designs (also available in an easier-to-read Advisory Circular: AC 20-169), which would be applicable to aircraft like the VC-25 ("Air Force One").