I agree with what Hale_bopp and Unique have said. Stimming can be a way to reduce anxiety. For me, it also helps me to focus. If your son feels the need to stim, it may not be because he is stimming that he is not aware of what is going on. It may be because he is already "drifting away," and he is using the stimming to bring himself back. This is something I tend to need to do. It is sort of like "recharging batteries."
I do not do anything that I think is too obvious, anyway, as far as stimming (though you say toe-walking is obvious, I guess others might notice I do this, then). For the most part, I tend to press my body against things, or I wiggle my fingers a lot, or I stare at different patterns of light. Perhaps you can encourage your son to find a less obvious way of stimming, so that atleast it will not look quite as "odd" to his classmates. As far as the not paying attention in school, try to find out what it is that is overwhelming him, and perhaps speak to the teacher. If he needs extra help, make sure it is offered, and maybe have the teacher write down assignments and such to be sure your son gets them.
Also, if your son does have Asperger's, it may not just be a case of stimming and zoning out that makes him feel "clueless." Sometimes it is difficult to understand what other people mean by their words, or even difficult to make out the words they are saying. It is possible your son is paying complete attention, or trying to, but just does not understand the way his teacher has explained things.