The SIGINT told them something was up, but they had more than just that.
Policies put in place by the criminal Clinton administration's minions, to protect their masters. So in practice, they had a lot of disconnected stuff from several sources, but no one analyst could simply look at all the available data and make the connection. The way you stated it makes it sound as though you believe that it was deliberately ignored to permit the attack to be completed. Please forgive me if I'm not reading you correctly.
As for deliberately ignored...Let me put it this way.
There is a certain amount of cognitive inertia present in any organization. The Bakken Fromation was well known and had even been produced in vertical wells in a few locations. Many of us urged oil companies to check it out further for decades prior to eventual horizontal drilling, not in the shale itself (done in the 1980s) but in the Middle of the formation where there are different, inherently porous but low-permeability rock types.
Finally, some smaller oil companies took that look, and the result has been over 600,000 BOPD of production and growing, and billions of dollars in economic development and profit. Overcoming the "way we have always done things" and conventional wisdom are difficult.
If you had intel prior to 9/11, having been told that Flight 800 was a "center fuel tank explosion" and not a terrorist act, that the Egyptian flight which was supposedly the act of single suicidal jihadi wasn't dodging a missile, would the concept that someone might use an airliner as a guided missile occur to you?
You'd get the "Yeah, right" horselaugh and comments about reading too much Tom Clancy. (In one of Clancy's books prior to 9/11, an airliner was crashed into the US Capitol during the State of the Union Address).
So, even if someone had figured it out, would that have been acted upon prior to 9/11?
Unlikely.
If you are going to stay one step ahead of an enemy who thinks outside the box, you'd better be able to think out there, too, or you are going to fail.