I have read The Commission and it is excellent. Of course truthers are only giving you one side of the story, when Shenon gives both. And when Shenon started to distance himself from the conspiracy kooks, well they were greatly disappointed. Yes a staffer was fired, but for legitimate reasons in not handling classified documents properly. Could it have been overlooked? Perhaps, but Zelikow's democrat counterpart, Daniel Marcus agreed with the firing. There were staffers fighting with Zelikow all the time, in fact Zelikow had to compromise on many issues that didn't go his way, and had to completely recuse himself from the investigation into the presidential transition. He also tried to push for an Iraq-Al Qaeda connection, and that failed. He also surprisingly attacked the administration when they weren't being forthcoming. This might stem from him being snubbed by Bush for not receiving a cabinet position. But he was good friends with Condi, and he did everything he could to not make her look bad.
As far as charities from Saudi Arabia funding terrorists, this is not news.
I'm no fan of Zelikow, and I don't think he should have been there. But obstruction of justice? Absurd. He may be an a-hole, but he is not a criminal.
If you want the true historical narrative of 9/11, I recommend The Looming Tower, Ghost Wars, Perfect Soldiers, The Shadow Factory, and Spying Blind. Also to dispel all the myths about the Bin Laden family, I would read Coll's The Bin Ladens. These are all books truthers avoid at all costs.