First, I believe there was a connection between Al Qaeda and Saddam. Second, removing Saddam earlier would not have affected 9-11. AQ's main base was in Afghanistan under the Taliban. Saddam was simply a kindred spirit who probably sent a little financial support and maybe some intel.
Speaking of Intel: The "community" was so downsized after the Cold War that we didn't have the capability we should have had to prevent 9-11. To put it another way, put a blindfold on a sharpshooter and see how well he fires.