This is by far the best critique of Fahrenheit 9/11 I've heard. I hate Bush, I love Michael Moore, and I hope his movie helps to depose the despot who has caused so much pain in the world.
However, I did think about the things you mention on the second viewing of the movie. I think this argument that Moore could have made a more coherent argument if he'd used some of the neo-con facts you mentioned makes the most sense. The thought that he could have made it even more powerful and accurate makes me wonder if he could have convinced more conservatives and moderates to vote against Bush by following your advice.
Which brings me to this conclusion. Knowing that Moore has said he appreciates constructive criticism, I suggest you contact him about adding some of your facts to the DVD.