Hi everyone, I can clear this up.
The USS Pennsylvania was Flagship for the entire U.S. Pacific Fleet, with CinCPac Kimmel on board.
The USS California was the Flagship of the Battleship Battle Force, with V.Adm. William S. Pye on Board.
There were also flagships of individual battleship divisions, I'll post them for anyone's interest.
BATTLESHIP DIVISION 1
Arizona (Flag), Oklahoma, and Nevada
BATTLESHIP DIVISION 2
California (Flag), Tennessee, Pennsylvania
BATTLESHIP DIVISION 3
(Transferred to Atlantic, 1941)
New Mexico (Flag), Mississippi, Idaho
BATTLESHIP DIVISION 4
Maryland (Flag), Colorado, West Viriginia