The two 747-based aircraft in the fleet were some of the last 747-200s built. They actually went into service long after the 747-400 arrived on the scene. I believe the outfitting contract was done at Boeing Wichita. It took years.
"Air Force 1" is only a callsign when the President is on board, otherwise the aircraft use their standard USAF callsigns. Both aircraft came to Teesside last year when the US President visited there, while for the mission taking him to Iraq one was used from Texas to Washington, then they changed planes to the other one for the Transatlantic leg. There must be some procedures that govern what gets used where.
There are a number of new 747s used round the world by state leaders (Japan, Saudi, etc) that also got done at Wichita. Some of the non-security items probably are used on those too.