The problem you have is the one shared by everyone from devotees of parapsychology to people who believe Meredith Kercher was killed in an orgy initiated by Amanda Knox: your prior on your theory is simply way too high.

Simply put, the events of 9/11 are so overwhelmingly more likely a priori to have been the exclusive work of a few terrorists than the product of a conspiracy involving the U.S. government, that the puzzling details you cite, even in their totality, fail to make a dent in a rational observer's credence of (more or less) the official story.

You might try asking yourself: if the official story were in fact correct, wouldn't you nevertheless expect that there would be strange facts that appear difficult to explain, and that these facts would be seized upon by conspiracy theorists, who, for some reason or another, were eager to believe the government may have been involved? And that they would be able to come up with arguments that sound convincing?

I want to stress that it is not the fact that the terrorists-only theory is officially sanctioned that makes it the (overwhelming) default explanation; as the Kercher case illustrates, sometimes the official story is an implausible conspiracy theory! Rather, it is our background knowledge of how reality operates -- which must be informed, among other things, by an acquaintance with human cognitive biases.

"Not silencing skeptical inquiry" is a great-sounding applause light, but we have to choose our battles, for reasons more mathematical than social: there are simply too many conceivable explanations for any given phenomenon, for it it be worthwhile to consider more than a very small proportion of them. Our choice of which to consider in the first place is thus going to be mainly determined by our prior probabilities -- in other words, our model of the world. Under the models of most folks here, 9/11 conspiracy theories simply aren't going to get any time of day.

If it's different for you, I'd be curious to know what kind of ideas with substantial numbers of adherents you would feel safe in dismissing without bothering to research. (If there aren't any, then I think you severely overestimate the tendency of people's beliefs to be entangled with reality.)