I’m pretty sure there are no missiles that punch a hole into their target like an artillery shell. They typically use proximity fuses. Look at the damage to Malaysian flight 17 that was shot down over Ukraine. It’s peppered with small fragment holes. Have you seen anything like that on TWA flight 800?
As for the missing section you mention, I have not heard anything about this. I’m pretty sure the sections from that area of the aircraft were the first pieces to break off and were in the “red zone” from the recovery area. That’s what led the NTSB to figure out that the explosion originated in or around the center fuel tank. (The yellow zone contained the front 1/3 of the fuselage which broke off afterwards, and the green zone contained the remainder of the aircraft which continued to fly a bit longer.)
Back to the missile theory. There is a poster on this thread that explained the rocket motors do not burn all the way up to the target, but for about three seconds, and after that, it would be impossible for a human eye to see the missile from ten miles away. Missiles with longer burns would have to have been fired by a large ship. With that in mind, who do you think fired the supposed missile? (The top two guesses on this thread are the Iranians and the US Navy.)
The FBI looked at the USS Normandy and there were no missing missiles, and it was out of range anyway. There has been no evidence of an Iranian warship in the area, and the MANPAD type weapon fired from a boat theory has been pretty much debunked due to range issues (and would also not fit with these eyewitnesses seeing a rocket motor firing all the way to impact). What is your missile theory?
The federal explanation is made of whole cloth. You believe it. That is on you.
The goverment will not say, "yeah, we made that shit up because it made us look really,.really bad during an election."
Nevertheless, it was a missle, witnessed by hundreds, in real time.