The 9/11 hijackers were mostly Saudis lead by a US-trained individual that was later found and executed in Pakistan, where the group was founded. The only way Afghanistan was close to any of this was geographically.
You (intentionally?) leave out the important detail that the main orchestrator of the attack bin Laden / al-Qaeda were based in Afghanistan and Taliban refused to extradite him/them.
They offered to extradite him if America could prove that he was responsible. This seems reasonable until you realize that the only way to do this would be to offer the Taliban, who never were allies, a list of most of the US' intelligence assets, so what would happen is they would either give OBL up or not but then would execute everyone supplying info.
It was easier and more expedient for GWB to go to war
Yes, Pakistan was, in a way, helping bin Laden to hide and evade the USA military. The fact that the USA never "tough talked" to Pakistan, even when the intelligence agencies left no doubt about that, is proof that Afghanistan was anything -but- legit.
Yes, they were hiding bin Laden and that was the causa belli. The USA gave an ultimatum to the Taliban, which they denied, and the invasion happened shortly after.
After the battle of Tora Bora, a lot of al-Qaeda members managed to flee into Pakistan and further east, so you could say that the reason for the invasion into Afghanistan ended there.
Yeah it's kinda hard to isolate sunni terrorism to a single location. America and Saudi Arabia funded a whole bunch of extremist madrasa in Afghanistan and Pakistan as a bid to oust the Soviet occupation.
This militant force was primarily led by Arab fighters who operated largely in and around Afghanistan and Pakistan. So the hijackers were mostly Arab, but a lot of their organizational infrastructure operated out of central Asia.