This is very complicated and subtle subject. Most of people who write and publish scientific papers does not have it, so they are imagining what it is and why it is so.
In my opinion it is just a "glitch" in forming some habits (in the initial training some Neural Networks), which results in biased perception and flawed models of reality. The simplest model could be that, we experience much higher emotional load in some social situations, such as forced eye contact, or unwanted attention from others (too old or sick or otherwise "unpleasant" people) while other people would not have any physiological discomfort. The key word to understand it is overwhelmed (there are also interference between different sub-systems of a brain, which produces tension and anxiety ). We are almost constantly overwhelmed by our own states, much like to have all the physiological symptoms of fear or panic without actual fear. We could say that behavioral patterns we develop is a result of some defense mechanism, attempt to compensate some inherited inability to deal with "emotional pressure". This does not mean that we are not sharp or unable to concentrate - it just requires lots of fine control and effort from us.
I am not going to argue about the exact nature of the Asperger Syndrome, except that it seems to me rather a psychological meme, a too rough model which trying to explain subtle behavioral differences. The too narrowly focused attention, restricted, repetitive behavior, some slight deviations in language usage and related social impairments, such as famous "mind blindness" are the effects, not the causes. The causes are still unknown, while "mechanics" is rather self-evident and could be altered with reasonable success by various re-training CBTs. At least I did it.
Here I will describe what I did and why, so some of us could suffer less, especially from not realizing what is wrong with the world and the people around them - very typical and genuine puzzle. The very first "big idea" to realize is that It is not the world is what is wrong, it is you. But it can be undone And, yes, most of people are assholes, this we have realized too early and too clearly. Ordinary people usually realize this in maturity, after good education, so they begin to understand forces behind some of social processes.
In some sense the path is quite similar to the one of Gautama, given that he was a historical figure. His realizations are quite similar to insights a mildly autistic person might have watching and trying to figure out what is wrong with the world. I even could say that the Buddha has been one of us. The natural tendencies for artistic attentive absorbing and rather analytic mindset, plus a deep dissatisfaction with social system are hallmarks of Asperger (unless constant abuse didn't ruin you).
All this might seem controversial and speculative, but most of us would find these my generalizations perhaps even too familiar.
The amateur CBT I have bootstrapped for myself is what I call 100% idle. It is a simple compilation of some ancient Oriental ideas and modern knowledge - nothing complicated, expert that it worked for me. This whole site is an attempt to make a big picture of how it may work and why. These text are profoundly unscientific, it is rather a naive, home-made philosophy. The reason it looks so clumsy is not because clumsiness is another our hallmark, but because I have made it on the go, without much hope that it would work.