I was interested in your defence of the "truther" position until I saw this this litany of questions. There are two main problems with your style of argument.

First, the quality of the evidence you are citing. Your standard of verification seems to be the Wikipedia standard - if you can find a "mainstream" source saying something, then you are happy to take it as fact (provided it fits your case). Anyone who has read newspaper coverage of something they know about in detail will know that, even in the absence of malice, the coverage is less than accurate, especially in a big and confusing event.

When Jack pointed out that a particular piece of evidence you cite is wrong (hijackers supposedly not appearing on the passenger list), you rather snidely reply "You win a cookie!", before conceding that it only took a bit of research to find out that the supposed "anomaly" never existed. But then, instead of considering what this means for the quality of all your other evidence, you then sarcastically cite the factoid that "6 of the alleged hijackers have turned up alive" as another killer anomaly, completely ignoring the possibility of identity theft/forged passports!

If you made a good-faith attempt to verify ALL the facts you rely on (rather than jumping from one factoid to another), I'm confident you would find that most of the "anomalies" have been debunked.

Second, the way you phrase all these questions shows that, even when you're not arguing from imaginary facts, you are predisposed to believe in some kind of conspiracy theory.

For example, you seem to think it's unlikely that hijackers could take over a plane using "only box-cutters", because the pilots were "professionals" who were somehow "trained" to fight and might not have found a knife sufficiently threatening. So you think two unarmed pilots would resist ten men who had knives and had already stabbed flight attendants to show they meant business? Imagine yourself actually facing down ten fanatics with knives.

The rest of your arguments that don't rely on debunked facts are about framing perfectly reasonable trains of events in terms to make them seem unlikely - in Less Wrong terms, "privileging the hypothesis". "How likely is that no heads would roll as a consequence of this security failure?" - well, since the main failure in the official account was that agencies were "stove-piped" and not talking to each other and responsibilities were unclear, this is entirely consistent. Also, governments may be reluctant to implicitly admit that something had been preventable by firing someone straight away - see "Heckuva job, Brownie".

"How likely is it that no less than three steel-framed buildings would completely collapse from fire and mechanical damage, for the first time in history, all on the same day?" It would be amazing if they'd all collapsed from independent causes! But all you are really asking is "how likely is it that a steel-framed building will collapse when hit with a fully-fueled commercial airliner, or parts of another giant steel-framed building?" Since a comparable crash had never happened before, the "first time in history" rhetoric adds nothing to your argument.

"How likely is it that the plane flown into the Pentagon would execute a difficult hairpin turn in order to fly into the most heavily-protected side of the building?"

Well, since it was piloted by a suicidal hijacker who had been trained to fly a plane, I guess it's not unlikely that it would manouevre to hit the building. Perhaps a more experienced pilot, or A GOVERNMENT HOLOGRAM DRONE (which is presumably what you're getting at), would have planned an approach that didn't involve a difficult hairpin turn. And why wouldn't an evil conspiracy want the damage to the Pentagon to be spectacular and therefore aim for the least heavily protected side? Since, you know, they know it's going to happen anyway so they can avoid being in the Pentagon at all?

If the plane had manoeuvred to hit the least heavily-protected side of the building, truthers would argue that this also showed that the pilot had uncanny inside knowledge.

"How likely is it that [buildings] would ... explode straight downward?" Well, as a non-expert I would have said a priori that seems unlikely, but the structure of the towers made that failure mode the one that would happen. All you're asking is "how likely is it that the laws of physics would operate?" I'm sure there is some truther analysis disputing that, but then you're back into the realm of imaginary evidence.

"How likely is it that this would result in pools of molten steel?" How likely is it that someone observed pools of molten aluminium, or some other substance, and misinterpreted them as molten steel? After all, you've just said that the steel girders were left behind, so there is some evidence that the fire didn't get hot enough to melt (rather than weaken) steel.