Mycroft:
According to declassified info mentioned in the Press and also in the book "Blind Man's Bluff," the Glomar Explorer was built by Hughes under CIA contract for the explicit purpose of digging up the Russian Sub. The project, it was said, was desguised as a mobile deep drilling rig for public consumption.
If you had carefully read "between the lines" of Aviation Week & Space Technology over the past 20 years, you would have some clues about secret payload shuttle missions.
Cheers