When I was on a Boeing tour in Renton a long time back, a guide told me the a/c are basically delivered as shells and the military finishes (or supervises) installation of everything including the avionics and flight controls. I don't know if this is true or not.
Sort of. Everett (if we're speaking 747s) builds the 747 shell, then it is moved on elsewhere for custom interiors. Boeing did the Presidential pair at their Wichita, Kansas facility. Many Middle East etc aircraft get done by Lufthansa Technik at Hamburg. By the way, they're more complete leaving Seattle than described. If you don't install flight controls, it's a bit difficult to move it somewhere else .... ! And speaking of flight controls, the reason the current Air Force Ones were basically 747-200s but built after the 747-400 went into production was doubt at the time about the security of electronic flight controls.
There are also assorted a/c based on 757-200s and 737NGs that are used for executive transport.
Bill Clinton when Pres used the 757 for shorter flights within the US, but this is apparently beneath Dubya.
ATC: "United 905 Heavy, proceed direct taxi point Kilo, behind VC-10"
UA905: " Er, Tower, by VC-10, do you mean that big grey thing directly ahead of me?"
Just tell him it's that thing that looks like an MD-80 on steroids.