After the narrative on the al-Shifa bombing, the report does note Clarke’s concerns about the Iraqi connection (sorry, working my way through this thing). Page 128:

“Though intelligence gave no clear indication of what might be afoot, some intelligence reports mentioned chemical weapons, pointing toward work at a

camp in southern Afghanistan called Derunta.On November 4, 1998, the U.S.

Attorney’s Office for the Southern District of New York unsealed its indictment

of Bin Ladin, charging him with conspiracy to attack U.S. defense installations.

The indictment also charged that al Qaeda had allied itself with Sudan,

Iran, and Hezbollah.The original sealed indictment had added that al Qaeda

had ‘reached an understanding with the government of Iraq that al Qaeda

would not work against that government and that on particular projects, specifically

including weapons development, al Qaeda would work cooperatively

with the Government of Iraq.’ This passage led Clarke, who for years had

read intelligence reports on Iraqi-Sudanese cooperation on chemical weapons,

to speculate to Berger that a large Iraqi presence at chemical facilities in Khartoum

was ‘probably a direct result of the Iraq–Al Qida agreement.’ Clarke

added that VX precursor traces found near al Shifa were the ‘exact formula

used by Iraq.’ This language about al Qaeda’s “understanding” with Iraq had

been dropped, however, when a superseding indictment was filed in November

1998.