1) People skeptical of the solidity of the science in AGW are not 9/11 conspiracy theorists. You're comparing one to the other because it makes your argument simpler. It's a meaningless and dishonest comparison. The questions don't go away simply because you call the questioner a Nazi.
2) It's not just the emails, though they are somewhat damning. People are looking at the code, and they're looking at the provenance of the information as well. It's not encouraging. It's certainly not "settled science". It looks more like "settled results".
3) Any rebuttal that begins with "you have to have a Ph.D. to understand why this number should be a 3 instead of a 4" smells funny. I don't have to have a Ph.D. in astrophysics to understand the basics of absorption line spectrums, because the explanation is straightforward and well understood. Hiding behind credentials is not a substitute for understanding thoroughly enough that you can explain the hows and whys and defend them.
I'm actually of the opinion that carbon emissions are not good, and we should do something about them. Carbon emissions make a fairly good metric for efficiency, and encouraging efficiency is a good thing. I object to grand, sweeping changes negotiated in the political sphere because once you introduce politics you can't disentangle it. Especially inside the global political sphere. Carbon emissions become a club to wield against political enemies and defend political interests, and it becomes decoupled from the environmental good.
So I'm in favor of continuing study of climatology, and to continue to work on the climate models. This is good science that we need to know. I'm in favor of establishing some kind of baseline to measure carbon emissions so we can make something like informed decisions. I object to climatologists needing to come up with doomsday scenarios to justify their funding, and I object to emissions legislation whose primary purpose seems to be redistribution of wealth. I don' think this makes me a 9/11 conspiracy theorist, nor a birther. Yet I think the current state of climatology is full of holes concealed by a lot of hand-waving.