1) al-Qaeda, from what I've seen in various documentaries, means "the base", or "base of Jihad", and was created by bin Laden and his mentor as a way to keep track of the fighters coming in and out of Afganistan-the CIA/ISI connections came later. As for the theory itself, I use to think that when you first explain shit to me, that after the neo-cons took power, they found out about the plot and made sure it was succesful. But the more I learned the less that made sense. Such as the fact that some of the hijackers are proven to be a live, some trained in U.S. military bases, some can't be accounted for in the U.S., ect...

2) The planning in conjunction theory also seems viable since bin Laden & Zawahiri have CIA ties, it's possible that they worked with the CIA on this attack not knowing they were doing so at the behest of the Bush Admin. I mean, if I were the leader of Hamas and had Mossad ties from back in the day, and they approached me of an operation to stage a massive attack in Israel, kill thousands of Jews, and me and Hamas would get the credit, your damn right I'd take it. All's I'd have to do is supply the suicide attackers and I would be able to go from killing a few people at a time to thousands, and I'd get the credit. Makes sense.

Also, been bin Laden has been quoted as saying "pray for your brothers" months before the attacks (possibly refrencing the Cole bombing) which shows he doesnt keep anything secret. Any one of the thousands who attend al-Qaeda trainning camps could have been a double agent.