Credit ravingnutter which disputes everything you posted from the 9/11 Commission report with regard to Atta:
In Washington, the FBI moved to quiet the Prague connection by telling journalists that it had car rentals and records that put Atta in Virginia Beach, Va., and Florida close to, if not during, the period when he was supposed to be in Prague. The New York Times , citing information provided by "federal law enforcement officials," reported that Atta was in Virginia Beach on April 2, 2001, and by April 11, "Atta was back in Florida, renting a car."
Newsweek reported that, "the FBI pointed out Atta was traveling at the time [in early April 2001] between Florida and Virginia Beach, Va.," adding, "The bureau had his rental car and hotel receipts." And intelligence expert James Bamford, after quoting FBI Director Robert Mueller as saying that the FBI "ran down literally hundreds of thousands of leads and checked every record we could get our hands on," reported in USA Today , "The records revealed that Atta was in Virginia Beach during the time he supposedly met the Iraqi in Prague."
All these reports attributed to the FBI were, as it turns out, erroneous. There were no car rental records in Virginia, Florida, or anywhere else in April 2001 for Mohamed Atta, since he had not yet obtained his Florida license.
His international license was at his father's home in Cairo, Egypt (where his roommate Marwan al-Shehhi picked it up in late April).
Nor were there other records in the hands of the FBI that put Atta in the United States at the time. Director of Central Intelligence George Tenet testified to the Senate Select Committee on Intelligence in June 2002, "It is possible that Atta traveled under an unknown alias" to "meet with an Iraqi intelligence officer in Prague." Clearly, it was not beyond the capabilities of the 9/11 hijackers to use aliases.
http://www.edwardjayepstein.com/PragueConnection.htm
I see a lot in the 9/11 report that is not disputed, such as:
"The FBI has gathered evidence indicating that Atta was in Virginia Beach on April 4 (as evidenced by a bank surveillance camera photo), and in Coral Springs, Florida on April 11, where he and Shehhi leased an apartment."
If you go to the link or just search the report, you will see that they provided documentation for these claims. Again, I'm not saying they are right. Just reporting what they said.