as for who the real mysterion is, someone posted this on yahoo answers:
There is a big clue that everyone seems to have overlooked- the fireworks used in Mysterion's escape from the Coon, as Cartman pointed out "they are illegal"- who has a history of illegal firework smuggling in South Park..? That's right- Stan's uncle Jimbo ("Summer Sucks"-S02E08), that's how Mysterion could get hold of illegal fireworks.
On top of this, for total proof- And as previously mentioned the "M" stood for Marsh. Kenny couldn't afford fireworks. He visited Kyle (counts out Kyle- but they've got to be good friends). Clyde was asleep in class when Cartman revealed the Coon's location. And Cartman didn't actually *say* he thought it was Wendy- when she suggests it need not be a boy he just exclaims "f*kin b**ch".. Also, Stan is unpredictable and highly secretive at times, like in "The Urinal Deuce"."
and something i noticed is professor chaos said that the body type had to be someone like stan or kyle, but the keyword here is "like" so that evidence isn't the best
But yes, I agree with your philosophy... In the past I've thought it was Clyde because Mysterion was out late and Clyde was asleep during class...but then I realized he wouldn't be paying attention to were The Coon would be if he was asleep. But Stan does seem like the right fit.