1) Through the day time, no AOA and POP are two separate buses EXCEPT after about an hour after closing.That is usually when they will combine routes.
2) Some do, some do not. I would not recommend traveling between 12pm-4pm because that is usually when they spread to about 30-35 minutes.
3) That is up to you. Sometimes, the parks will have 3 or 4 buses that follow each other to resorts, sometimes its a 30 minute wait.
When I was in Transportation, the routing program would do funky things like that, and sometimes there is nothing you can do. If you are staying at AOA or POP, the parks tend to run more buses in the morning, and you will see a Transport CM out in the load zones communicating with the Transport Dispatchers informing them with what is going on.