The FBI had a list of suspects from the manifests almost immediately, but confirming these were their real identities took longer. So the first list they put out on September 14th contained names and a few biographical details only, no pictures.
They knew some of the hijackers were pilots. But which ones? Public record searches led them to people like Waleed Ahmed al-Shehri; a pilot, a similar name to one of the people on the passenger manifests (Waleed Mohamed al-Shehri), who had trained in Florida at a time when the first pilots were in the country.
The FBI weren't officially releasing pictures yet, but either some were leaked to the media, or the media uncovered them for themselves. On September 16th 2001
a CNN report ran some of these, with pictures of the wrong individuals for Wail al-Shehri, Abdulaziz al-Omari and Saeed al-Ghamdi. I believe the first one was of Waleed Ahmed al-Shehri, and all three men came forward in the next day or two to say they had seen their photos in the press but this was nothing to do with them.
There were several similar stories around at the time, though not so definitive. Like this, for instance:
Confusion Over Hijackers' Names Hindering Investigation
The original listing prompted a Salem Ibrahim Ahmed Alhazmi, who works at a government-owned petrochemical complex in Saudi Arabia, to step forward and say that he had never been to the United States. He also said his passport had been stolen by a pickpocket on a trip to Cairo three years ago.
[Chief of the Saudi Embassy's information office] Allagany said he is still counting this Alhazmi as someone whose identity had been stolen. He did not consider the difference in middle names and initials between Salem Ibrahim Ahmed Alhazmi and Salem M.S. Alhazmi to be persuasive.
Washington Post, Oct 7, 2001
This Salem Ibrahim Ahmed Alhazmi has a different name to the hijacker, and doesn't explain how he matches the suspect in any other way. So how can we tell it's the same man?
Notably all these stories appeared before the FBI released an official list of hijacker photos on September 27th. After that, nothing, at least as far as I know, so the whole thing was over in less than two weeks.
This was enough for the truthers to run with it, though, and they now not only repeat these old stories, but pretend they are solid proof. David Ray Griffin said in "The 9/11 Commission Report-Omissions and Distortions", ofor instance, that the hijacker identifications have been "shown to be incorrect". Nafeez Ahmed has claimed "it is now known that at least 10 of the 19 alleged hijackers are alive according to multiple, credible news accounts by the BBC, CNN, the Telegraph, the Independent, and other international media."
You won't see people like Griffin explain why the supposedly still-alive Saeed al-Ghamdi has appeared in at least two al Qaeda videos, though, including a video will where he says:
"You will be turned into pieces because of the mujahedeen," he said. "And I tell you that we are preparing something for you. God will punish you in a big way. And we promise the United States of America that we will stop you, that we will hurt you -- and we will make sure that you don't have any peace."
Found at
http://www.cnn.com/2003/US/09/12/hijack.tape/index.html
I've also never seen a truther book address the fact that in 2002 Saudi Arabia confirmed the US list:
Previously, Saudi Arabia had said the citizenship of 15 of the 19 hijackers was in doubt despite U.S. insistence they were Saudis. But Interior Minister Prince Nayef told The Associated Press that Saudi leaders were shocked to learn 15 of the hijackers were from Saudi Arabia.
"The names that we got confirmed that," Nayef said in an interview. "Their families have been notified."
http://www.usatoday.com/news/world/2002/02/06/saudi.htm
They also have no explanation for media reports from families of people like Wail and Waleed al-Shehri, who even if they don't believe they were involved, still accept that they were involved. Other than the standard excuse of "well it must be a lie", that is.
But the reality is if you look at everything then there's plenty of evidence to support the FBI list, and extremely little to support the "still alive" claims. Most truthers know this, which is why they don't make such a big deal of it any more, and I think over time it'll just fade away. In the meantime, you'll find more points and sources for the above
starting here.