Clarke is saying that Clinton had institutionalized a set of governmental routines for dealing with heightened threats from terrorists. He is not saying that Clinton bequeathed a "big think" plan to Bush on terrorism. He is saying that he bequeathed the Bush administration a repertoire of effective actions by high officials.
He thinks going to such a heightened level of alert and concerted effort in 2001 might have shaken loose much earlier the information that the CIA knew that Khalid al-Mihdhar and Nawaf al-Hazmi were in the US. As it is, the INS wasn't informed of this advent and did not start looking for them until Aug. 21, 2001, by which time it was too late. Since they made their plane reservations for September 11 under their own names, names known to the USG, a heightened level of alert might have allowed the FBI to spot them.