1). They mistake evidence for fact and mistake models based upon evidence for fact. The theory of evolution is a perfect example. We have a large set of evidence and people interpret this evidence to support evolution. However, utilizing the exact same set of evidence we can formulate an equally valid, opposing theory, namely one in which evolved states of consciousness lead to evolves physical states rather than vice versa.
Actually, it's all just statistical probability in a world of chaos. If we pick up a ball and drop it, there is a close to 100% chance that it will fall towards the gravitational center of the nearest body with the most mass. We know this not so much through interpreting observational evidence, as through figuring out the actual mechanics of the process. Likewise with evolution, the reason that theory allows us to predict what happens to species with such great accuracy is not so much because we have observed it in the past, and believe it will happen again just because it has happened before, but because through observation we have figured out the actual mechanics of the system, the parts that make it work, and why. We understand that if this shifts to that, and this becomes that, the end result will most likely be so-and-so. It's the difference between stating that a lever works in a specific way because you have seen it work in a specific way, and knowing that it works in a specific way because you know and understand the laws of physics that the lever, and everything else in this universe, has to follow. Due to this, I can't see how we can formulate an actual conclusion for the mechanism of evolution of consciousness. At least not beyond the "brain evolving as a computational machine."
3). They neglect experience as a means to knowing. This is often ironic in that many atheists also claim things like 'truth is relative' or 'logic is abstract' and then utilize abstract interpretations of evidence to deny the existence of god.
As in reply to #1, experience does not mean knowing. Plenty of people experienced solar eclipses, and claimed to know what causes them, but it wasn't until we actually discovered and studied the mechanism of our solar system that we actually knew. And those who don't know how our solar system works, still won't be able to figure out solar eclipses just by experiencing them.
4). They adhere to Cartesian dualism by which it is asserted that there is an unbridgable chasm between mental and physical reality.
I think atheists simply reject the idea of a "mental" reality; at least in a sense of there being anything spiritual, or beyond our physical world.
5). They emphasize the importance of math, but they fail to realize that the most basic algebraic structure is language. In fact, every identifiable object or concept is, by definition, its own language. "In the beginning was the word" is true as fuck. Language (I.e. syntax + content + grammar) lays the foundation for all of reality, and it is far more important to have a solid grasp of syntactic operations than to know how to calculate specific math problems or formulate models. You can't understand the universe without understanding language because the universe IS a language.
Not sure what you are trying to say here, because it sounds like you are claiming that before language (actual language, involving words and such), nothing could exist. Yet we know things existed for millions of years, reality and all, before humans came along and invented language. There was a ton of other communications methods before then, and some of them unconscious even (meteor hit moon, mood change orbit, signal received). Maybe you can restate this a bit differently?
6). They use words like "supernatural" to refer to religious claims, but then they forget that 'chance' and 'probability' are just alternative words for unknown specific causation. Furthermore, they experience cognitive dissonance in light of paradoxes which, contrary to popular belief, are self-resolving rather than impossible.
Chance and probability are not unknown, nor supernatural. It just means that either of two or more options can happen, and we can't predict which, but we do know what has happened after it has. E.g. you can drop metal filings all around a magnet, expecting then to fall into perfect spheres around the edges of magnetic lines, but many of the filings will fall a bit off, or in a weirdly turned way. We can't predict that, but we can easily explain that it was due to air resistance, some of them bumping into each other, and outside magnetic interference. Totally random chance probability, but nothing supernatural or unknown.
7). They mistakenly study reality as if it is the input of our experience when it is actually the output of internally processed information.
Do you believe the universe can exist without us being there to observe it? If yes, then I'm not sure how you can hold the view that reality is the output of our internally processed information. (If a tree falls in the woods, and no one is around to hear it, does it make a sound?)
8.) They don't understand the relationship between subjects and objects in the universe, or at least they cease their understanding when objects are in close proximity to the subject. For example, they will instantly assert they are different from a tree (an object) but not different than, say, their body (also an object). This is a problem when they then assert that the death of the body equates to death of the subject.
That's actually the thing that has been confusing people for millenia, making them think that they are somehow apart from their bodied, just existing in their heads and using their ears and eyes to look out into the world. I don't know about other atheists, but as one myself, I claim that, yes, I am different from a tree, in a sense that the tree is an organism with it's own system, but I am not very different from my body, in a sense that my body and my consciousness are all part of the same organism, linked directly together through the nervous system. The tree and my body both exist in the same system, planet earth, but that doesn't make the computational part of my organism that gives me consciousness a part of the tree.