I was reading your post when a thought hit me:
I was working on a case once where a boy who had always acted appropriately reached puberty. Everything was working correctly in the hormonal area, but the area in his brain that controls his impulse control had not matured. Once puberty hit the boy was suddenly acting inappropriately and was having difficulty controlling himself due to the lack of maturity of the impulse control region of his brain.
I'm certainly not saying this is your son's issue. However, I do know that impulse control issues run in some of our children. For example, my son is 11, but many times he acts like he is eight when it comes to impulse control.
It could be a puberty issue. It could be an impulse control issue. It could be a sensory issue. Those can all be worked on. However, it's important for him to know that there are boundaries, and running around the house nude is not allowed. Explain to him that everyone is entitled to their privacy, and that our nude body is a private thing. Give him his options of where he is allowed to be nude, but other than that he must wear clothing.
Good luck!
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A foolish consistency is the hobgoblin of small minds. ~ Ralph Waldo Emerson