Thoughts, in no particular order:
Both players need to sink the carriers at all costs. Duh.
If the Japanese player has been readying for an strike on Pearl Harbor, he's basically in the same position as Nagumo at Midway, right? Planes loaded with the wrong weapons and enemy task forces in the area. However, I doubt the Japanese player would have done that, because his scouts failed to give him an idea of forces in Pearl Harbor, and betrayed his presence.
The Japanese scout plane recognized three battleships in Pearl Harbor. This might get back to my "false recognition" question, but do the wrecks of the USS West Virginia, USS California and USS Arizona *look* like battleships? (I can't imagine anyone mistaking the USS Oklahoma for an operational warship) The USS Nevada was apparently refloated the 12th of February, at which point I assume she would be mostly indistinguishable from an operational ship. If they are operational battleships, I have to wonder why they didn't put to sea. If they aren't, the Japanese admiral still has to worry about tripping over a battleline of half-a-dozen dreadnoughts.
However, if the US battleships are in fact operational, the Japanese player has a pretty good idea of the location of pretty much all the USN forces which is a tremendous advantage.
What's with the USN transports? They can't score any victory points by making landings on Japanese islands, can they? They do make for nice juicy targets for the Kido Butai though.
The two Japanese carriers could be a decoy force. There might be 4 others getting ready to bomb the heck out of Midway and support a landing. Heck, they could be light carriers, opposed to the fleet carriers. Or the light carriers could be the ones supporting a Midway landing. Multiple fleet carriers is a bit large for a diversion though. Japanese carrier doctrine, as well as basic rules of warfare would advise concentration of force. Also, the American player doesn't know the location or status of the Japanese battleline.
I think the Japanese player is in a respectable position to defeat the USN in detail. Unless of course he's "Nagumoed" himself.
Edit: Which ways are the winds blowing? It would be a tremendous advantage for the Japanese player if the Americans had to sail towards the Japanese forces and the presumably accompanying Kongos to launch aircraft.
Edit #2: what is the specific date of this battle?