I would model the situation as it existed about a day before the first attack on the island of Midway. Japanese forces required to adhere to their doctrinal search pattern, which was deficient. Basically, both forces required to adhere to their existing doctrine at that time. Japanese aviation superior at that time due to American inexperience in countering Japanese dogfighting (with hit-and-run tactics). American fire and damage control operations superior to the Japanese. Japanese and American flight operations very different.

There is still a problem that we know where the American forces were and when they were encountered. Probably would need an option for an ahistorical start, where the American carriers could navigate from Pearl to a different location off of Midway.

Further options: allow the Japanese to have Shokaku and Zuikaku participate in the battle (assume they were not damaged in the Battle of Coral Sea); allow the Japanese to structure their attacking fleet differently; etc