New here + question about physical activity

Hello
Not sure I posted in a correct section, feel free to move this if necessary.
My name is S. and I've got a son, Emin, who is 6 years old and was diagnosed with DMD about half a year ago. I've been lurking around this site for a while, but never posted anything yet.
Em has classic autism, which he was diagnosed with when he was 3 years old. He's non verbal and we're dealing with a lot of issues. His communication is very limited, as is his understanding.
He has been in the hospital for more than a month because of h1n1 and had quite some complications related to that (sepsis). After coming home from the hospital, he was very weak for a while, could hardly walk, could not stand up on his own. However, after a month, he's now doing great health-wise. He can get up, he can run around and walk.
 Trouble is, he runs too much. Yesterday we were outside and there was snow-he is terrified of snow, because it makes him wet and he has a horrible water phobia. Any other day, he would probably just scream and had a meltdown after seeing the snow, but yesterday he ran around with his brother, laughing all the time and enjoying it like I never thought he would. After about two hours of constant running I knew it was enough, but at the same time he seemed so happy and I haven't seen him laugh for a while.  So today, he has been screaming all day, pointing at his legs. I assume his muscles must hurt a lot and I feel horrible. I knew I shouldn't let him run around so much.
So...my question is this. How could I make a non verbal child, intellectually at about 2 years of age, understand when it's enough? Once he starts, it's very hard to stop him, he just continues to run around and smashes into things. If I hold him and try to calm him down it can quickly turn into a meltdown.

Frost