Several of the authors I've read have stated that the Japanese were very "offense" minded and that shaped their thinking in several ways. One result was that they disdained armor and other protection for their fighters, choosing to sacrifice protection for speed. Ultimately the availability of radios in every US fighter, armor protecting the pilot and self sealing fuel tanks (and the "Thatch Weave") allowed us to hold our own until the Hellcat arrived.

Another result was to focus on more militarily "worthy" targets such as capital ships and believing that attacking logistical and infrastructure was not as worthy.

Admiral Nagumo should in all probability have risked a third attack on Pearl Harbor with an emphasis on crippling the repair facilities and destroying the fuel reserves. Despite the fact that a "prepared" defense would no doubt have inflicted higher losses than those sustained during the first two attacks, it is extremely likely that in doing so, he could have significantly affected two key pieces which contributed to his later defeat at Midway.

That is not only the ability to launch the Doolittle raid and send out units to fight at the Coral Sea (both of which actions had contributing consequences to the later battle at Midway) due to the availability of plenty of fuel, but had the repair facilities been destroyed, Yorktown (assuming she DID fight at Coral Sea and sustained the same damage) would never have been able to be repaired enough to be available for Midway.

But of course hindsight is always at LEAST 20/20.

It has been quite a while since I got into the weeds on Pearl Harbor, but if memory serves me well, Nagumo never seriously considered a third strike on Pearl, and it was largely a figment of Fuchida's literary imagination in his early work, "Midway, The Battle that doomed Japan".

Like I said it's been a long time, so if my memory is faulty, please tell me. I don't mind being mistaken. I do mind being mistaken about the same thing twice

Even if the Japanese had been able to win at Midway - given your scenario - they ultimately would have lost the War. Maybe it would have been in 1946, but the Japanese lost the war on December 7th.

Had they attacked the various European possessions in the Western Pacific, including the Philippines, even forgoing the surprise attacks, two things probably would have happened.
1 - There initial strategy would have still succeeded. None of the combatants really had the resources to affect the outcomes of 1942.
2 - The US might have been willing to accept some of the conquests, or at least fought a less than total destruction war against the Japanese. Some form of armistice would have been reached, especially if the Japanese were seen as anti-communist.

But the surprise attack on Pearl gave the US no choice but to fight for the complete and utter defeat of Japan. The A-bomb would still have been developed and the US would have found a way to start using it no matter where its forces were in 1945. (I suspect the development of a 16" atomic warhead would have been accelerated) The US fleet still would have had a major numerical edge over the Japanese and the US Navy would have been able to sell the idea of just starving the Japanese.
It might have taken another year, maybe 2, but then more than 2 cities would have been turned to atomic ash, the US most likely would have had no qualms about using nerve & mustard gas against Japanese military targets. Instead of Island hopping the US might have just turned Japanese held Islands into Atomic Rubble.