This story has a familiar ring to it. Seems that the factory had a habit of leaving things back there. Here is a true story about 1965 GT350 5S003 (the first GT350) and the original owner. It is from 1965GT350mustang web site. Great place to visit.
http://www.1965gt350mustang.com/history.html
"A short time after purchasing 5S003, Moir heard something rattling near the back of the car. The noise was tracked down to beneath the rear shelf, when the rear shelf was removed an unused 289 Weber intake manifold was found! My only thought is that a Shelby American employee placed the intake in the back of 003 and when a co-worker was putting in the rear shelf perhaps his line of sight was blocked by the size of the shelf and the intake was covered over. "