Flaws in the book? Let's take the chapter on "The 9/11 Report and Vice President Cheney".
When he comes to talk of the "many serious problems, first raised by members of the Family Steering Committee, that the 9/11 Commission Report, like the Kean-Hamilton book, simply failed to address", the following example he provides is... the "hijackers are still alive" story. By way of support he selectively quotes Robert Mueller from September 20th saying the identities were in doubt, and doesn't tell his readers of Mueller's later statement that the questions had been cleared up.
His next example is the usual "why didn't the 9/11 Commission discuss the collapse of WTC7", hardly a surprise as they weren't set up to do that and no-one on the Commission was qualified.
He says Dick Cheney was the source for the order grounding planes and the shoot-down order, but in my view fails by a very long way to prove that.
He joins David Ray Griffin in pretending that Cheney saying "when I arrived [at the PEOC] within a short order, we had word that the Pentagon's been hit" means he arrived in the PEOC before the Pentagon was hit.
He places heavy reliance on Richard Clarke's timeline, despite its obvious flaws (talking to Myers in the NMCC when he was actually with Max Cleland, for instance).
He places very heavy reliance on Mineta's testimony, despite its even worse problems (as discussed here many times).
He seems to think the "phantom flight 11" issue wasn't discussed in the 9/11 Commission report.
He assumes, I think, that the phantom flight 11 was flight 77? I need to read it again, might be wrong there. Anyway, he mixes it up with flight 77 in a confusing way and seems to imply that it's the plane Mineta says Cheney and "the young man" spoke of later. Nafeez Ahmed does something similar, using the phantom account to pretend people were tracking Flight 77 on radar long before the Commission said, but that's incorrect. These are different reports from different sources and the phantom wasn't on radar.
He says the June 2001 intercept rule changes placed a new requirement forcing approval by Rumsfeld before intercepts could be launched. Wrong.
He reports Mike Ruppert's claim that Cheney was responsible for this through the Office of National Preparedness, and impressively says this hasn't been challenged. This is just the claim that Cheney was "in charge of NORAD" on 9/11 and there's not a jot of evidence to support that.
That's not an exhaustive list, but I'm busy so it'll have to do for now.