Agree with most of what's been posted, to which I'd add, attack the power station (on which everything depends), the Sub Base, and the Engineering & Repair shop. (Blowing up the torpedo store could be a net plus for the Sub Force.) An attack on the old Admin Building would be a real plus: Hypo was in the basement.
Contrary to what you might expect, this could be worse for Japan than what happened OTL. It puts pressure on Nimitz to build up at Midway, with base facilities (esp fuel), to take up slack from losses at Pearl. And, since carriers are no longer right to hand, close recce of IJN bases is a waste of effort; perhaps Nimitz can be persuaded to switch to mining them by subs (for which the old Bass, Bonita, & Barracuda are well-suited, & Argonaut purpose-designed), while using direction-finding to monitor movements of IJN minesweepers. (Then shoot the 'sweepers.)
If this puts more subs in Home Waters, Luzon/Formosa Strait, & Yellow Sea, Japan loses the war sooner than OTL...
Contrary to what you might expect, this could be worse for Japan than what happened OTL. It puts pressure on Nimitz to build up at Midway, with base facilities (esp fuel), to take up slack from losses at Pearl. And, since carriers are no longer right to hand, close recce of IJN bases is a waste of effort; perhaps Nimitz can be persuaded to switch to mining them by subs (for which the old Bass, Bonita, & Barracuda are well-suited, & Argonaut purpose-designed), while using direction-finding to monitor movements of IJN minesweepers. (Then shoot the 'sweepers.)
If this puts more subs in Home Waters, Luzon/Formosa Strait, & Yellow Sea, Japan loses the war sooner than OTL...