No, those are your factoids and assertions.
Flight data and voice data are not always recovered after an accident. That they weren't recovered or working after slamming into a building, burning for awhile with much more fuel (the building contents) than there would be in a typical crash, been in the middle of a building collapse, then smoldered under the building rubble for weeks, surprises me very little.
But you find it suspicious. I think that says more about your reasoning ability than it does about the plausibility of any particular scenario.
A changing transponder code. So? It was a trick. It worked. I would like to point out that since autopilots can't change the transponder code, the changing of the code contraindicates a remote-controlled takeover.
Your opinion: no one with the experience or the skill to fly the plane was onboard.
My opinion: No great skill at aviation was required or demonstrated in the flight.
Frankly, I think they were overqualified.
I'd bet money you could:
Take virtually any student that has soloed a Cessna 150.
Train him using only commercially-available-for the-PC flight sim software as a procedures trainer. I don't think much of them as simulating real flying experience, but for drilling on knob and switch placement and following procedures, they'd be perfectly adequate.
Put him in one of the 6-degree-of-freedom simulators, and he would be successful 3 times out of 4 attempts.
In point of fact, ISTR someone in the Netherlands doing something similar, though I don't have a link handy. The student was successful 3 out of 3, no problem, with far less than months of study and no religious convictions driving him.
Serial numbered parts: Would you really accept any information released to you by the the U.S. government on serial numbers of parts found while investigating the attack?
If your answer is no, then why even ask about information the existence of which is not going to change your position?
If your answer is yes, you would, then why is the DNA identification of twelve of the passengers not sufficient to uniquely identify flight 175?
DNA is a lot harder to forge than serial numbers on mechanical parts.
The passport from a different aircraft: that doesn't make it impossible for an adequate suicide pilot to be on board Flight 175. But it has such a nice emotional appeal to it.