Connections were never severed with the Arab Foreign Legion that was founded in Afghanistan, and despite a page full of lies on the U.S. State Dept. website, the U.S. recruited and trained the "Arab Afghans" through the CIA and other military and Western intelligence proxies and allies. (I used to have some respect for Milt Bearden, but he is clearly lying on that web-page. Perhaps Steve Coll was more accurate in his portrayal of the old Bearden than we know.)

Control of the Arab Afhgans and thus, "al-Qaeda", continued unsevered throughout the late 1980s and the entire decade of the 90s, (yes, under Clinton's administration), and it is documented by British author, Nafeez Mossadeq Ahmed, here:

Ties With Terror: The Continuity of Western-Al-Qaeda Relations in the Post-Cold War Period

I do not propose a theory to explain the U.S. Embassy bombings or the bombing of the USS Cole, but I believe that in time, it will be revealed that Western intel knew a whole lot more about those incidents than is publicly acknowledged.

Why did Western intel maintain connections with these mercenaries?

In a word, OPIUM. The Muj had their hands on the levers of opium control, and Western intel had their hands on the Muj. Post-U.S. invasion Afghanistan has seen a skyrocket in opium production, and now, in Iraq, opium production is taking off. (See this article at Counterpunch.)

U.S. invades, opium production skyrockets. What a coincidence.

The duplicity of Western intelligence assets and allies is notorious, but seldom remarked upon in the corporate press. A prime example is the gathering of right-wing maniacs at the Jerusalem Conference on International Terror back in 1979.

At the same time that the CIA rolled out covert action in Afghanistan, preceding the Soviet invasion, George HW Bush was in Israel reifiying the notion of "International Terrorism".

We are being played like puppets, and the masses are blissfully ignorant of almost all of this info.

Blowback doesn't really fly for me. It suggests a loss of control, (this is at least implied), but I don't believe the control was ever lost.