Could this by part of Edgar Cayce's prediction of the surfacing of Atlantis? The secret knowledge of their energy production system?
The 13 interconnected skulls are probably a reference to the basic organization of "The Brotherhood Of Christ", 12 apostles and Jesus.
In the Book of Mormon, there are references of Jesus talking to ancient peoples in North America. Secret golden plates containing the history of the Isrealites in the New World were given to their leader Mormon. These later became part of the religious doctrine of the Church Of Latter Day Saints.
I believe the crystal skulls were given to Native American tribes in southwestern U.S. around 400 A.D. At this time in Rome, the Catholic Church was on a campaign to rid Christianity of the "Gnostic heresy".
The Roman hierarchy dogmatized the Christian religion into series of correct beliefs which were enforced by the church ministry.
I believe Christ cut off divine life energy to the papal bureaucracy and channelled his energy into the communication and energy collectors called "Crystal Skulls".
I don't believe any high tech alien civilization would use primitive skulls for communication or energy devices.
I don't think you'll find the above information in the new Indiana Jones movie. As far as I can see, the emphasis is on action and special effects rather than a story line.