Of course this bothers me, but that does not make me susceptible to becoming a paranoid conspiracy theorist like Nixon or Hitler.
Don't forget McCarthy.

I understand your points, but this isn't conspiracy theory. Look, I don't think any reasonable person is suggesting that a there is widespread complicity on the part of most people in government service. That taxes the imagination of even the most creative.
But during the Soviet cold war era, there were numerous spies, reaching into the highest levels of government, working for the Soviet cause and against the interests of the American people. It doesn't require too much imagination to believe, using history as our guide, that there were those within the highest reaches of our government who would be willing sacrifice a few Americans if it advances their agenda. The intelligence "failures" were just too many.
Let's just take Coleen Rowley for instance. Now she tried over and over again to get a warrant to check Zacharias Mussoui's computer, and was completely rebuffed time and time again. What's interesting is that, as a last resort, she went to the CIA with pertinent information. (What that was, we'll not know for quite some time, it's been classified.) But it does raise an interesting point: Would you go to the CIA if you didn't have hard information? How would that go? "Hey, I captured a guy who was learning to fly airplanes. But ... he's Arabic. I'm with the FBI, but they won't issue a warrant. Maybe you should check into it." She would have been laughed out of town! The only reason she would have gone to the CIA was if she had HARD, CREDIBLE information.
So lets put two and two together. She needs a search warrant to make the evidence
admissable. That doesn't mean she hadn't read it. If she had read it, that would explain her hard information that she relayed to the CIA, (still classified).
With it being classified, I can't prove that the FBI and the CIA knew a sufficient amount to stop the attacks. But that is precisely the allegation that Ms. Rowley made. And if they knew, why did they not issue the warrant, or at least act to take Zacharias' friends into custody for questioning. Someone sat on that information.
You might call it an "intelligence failure" ... but shouldn't Congress at least investigate a failure of such a magnitude for possible intent? They could have access to the classified information simply by issuing a Congressional subpeona.
Caleb