He felt his business education was incomplete, so Eaton attended the two-year MBA program at Stanford where he specialized in small business finance and accounting. While at Stanford, Eaton also studied classical guitar with teacher Charles Ferguson.

The first years after formal education were critical in developing Eaton's artistic perspectives. Family and academic commitments fulfilled for the moment, he could at last embark on the personal quest which had been taking shape during his school years. While engaged in the Roberto-Venn work, he read omnivorously and investigated the spiritual and philosophical disciplines of many cultures. He spent days and nights outdoors, deep in the mountain areas outside Phoenix. He slept under the stars, living out of his car for two years. He contemplated the origins and dynamics of music. He wandered in the desert, and explored the ideas of "erasing personal history" and "stopping the world". He began to imagine and create the remarkably innovative instruments for which he is noted.

While this was not a time for performance before large human audiences, he began playing pieces in a variety of solitary settings, on a cliff in the moonlight by a quiet pool in a shadowed canyon. This period of Eaton's life is a source for much of his subsequent work, and the subtle qualities of sound, light and air experienced in the desert can be felt behind his every note.