How?
It is my understanding that the vast quantities of fuel at Pearl are primarily stored in huge underground caverns, far below the ground.
Not completely.
Most of the Pearl Harbor oil tanks were exposed to air attack.
Don't know. I've seen aerial photographs of huge tank farms at Pearl in 1941. Regardless, Nagumo should have pressed the attack until he was out of ammunition and fuel. He should have come home without one round of ammunition and needing a tow into port. He was afraid of being jumped by U.S. carriers, (whom he could not account for) but he would have been sailing flank speed for home (and the rest of the Imperial Fleet) as soon as the attack was finished. Besides, it's unlikely that the U.S. would have been able to mount a meaningful pursuit, or even if they could that they would have risked their remaining fleet in what might have been an ambush.
I think if Yamamoto could have had a Mulligan, he would have ordered the invasion of Hawaii, not just a raid.
Roosevelt ordered the Seventh Fleet be deployed from San Diego to Pearl personally. (He had been Secretary of the Navy during WWI). Clearly this was an enormous blunder.