Kimmel could shift his flag and command from sea

Could Kimmel command at sea if his usual flagship were in dry dock?

Yes. He could transfer his flag to an alternate command-capable battleship and would probably sail with the battle line.

Admirals routinely shifted their flags, and staffs planned alternate ships with the necessary command spaces and radio facilities. Because this scenario sends nearly every available ship to sea as one large formation, the prewar-minded Kimmel would probably command from a battleship with the battle line. Pearl Harbor was still treated as an administrative headquarters rather than the natural place to direct a wartime fleet. Later distributed task-force warfare made shore-based coordination more common, but the older custom placed the fleet commander at sea. USS West Virginia is one plausible alternate flagship, although the command practice matters more than the specific hull.