"The one in Pennsylvania was shot down." - Oh No it wasn't, according to eye-witnesses and the aircraft's flight recorders, the aircraft crashed up-side down but intact.
"It's debris was spread over miles...consistent with in-flight break-up." I could well imagine that an aircraft of that size crashing at 500+ knots would spread debris over a large area. One of the things that would have been consistent with in-flight break-up (as in the Lockerbie incident) would be bodies spread over that same large area. However all bodies from this flight were recovered from within the crash site crater, again indicating that the aircraft was intact at moment of impact.