Question on the dive times per day on each. Is each day based on the incoming high tide for the passes?
For diving the passes with the incoming tide, yes, the time each day may vary. However, when the incoming tide times are not right - an outgoing tide, for example - the operators usually dive the sloping wall outside.
If we wanted to stay in Fakarava north and dive the south pass, how should I pick the best days based on the tide charts?
I could try to guess but I'd be safer if I contact the dive operator and ask them in advance.
On a normal day, it takes about 6 hrs for the tide to go from low to high. For simplicity, round that up to about 6 hrs of incoming. But not all of it is usable because the speed of the current starts slow, gradually increases, peaks, and then gradually decreases. I speculate that the dive operator has to look at all of this and see if he can fit two dives in with a one-hour surface interval in between, while not having to leave in the wee hours of the morning or getting back in the early evening.
Using your example, I'd say you are correct in saying that a 6:24am high tide would not work. Conversely, the reverse of your example - ie, low tide at 6:24am, and therefore the next high tide at around 12:30pm - would probably work. After a brief low tide slack, the tide would start to slowly come in. Taking this a few steps further, if the dive operator leaves the North at 7:30am and arrives at around 9:00am, by then the incoming current should be close to peaking in speed. If he finishes the first dive at around 10:30am, and does a one-hour surface interval, there may be enough time to do a second dive with an incoming, albeit a bit weaker as it approaches the 12:30pm high tide.