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Just for accuracy:
1964 Wilderness Act
Representative John Saylor, R-Pennsylvania, was one of the first Members of Congress to advocate legislation that would protect land in its wild, unspoiled condition. His Act created the National Wilderness Preservation System. The Wilderness Act preserved large areas of our nation's lands into designated wilderness areas. Saylor's original 9.1 million acres of wilderness lands have been expanded over the years into today's 104 million acres, which form 631 wilderness areas in 44 states.
source:The Center on Congress, Indiana Unversity 
Explain undoing of deletion of California Consdierations - There were political considerations - At that time, most California politicians would not have suppported the 64 WA if it had included the San Joaquin Canyon. You are confusing exclusions within the Act with agreements made between politicans to get the Act passed.