I think John Scott would win this. For Scott, he had to toil in the minors for years, and had to fill the roll of enforcer. He was in the same system as Boogaard (RIP) and so he learned what he needed to do in order to make it to the NHL.
Chara on the other hand, made it the NHL quicker because he had the skill to to play regular minutes, versus minutes as an enforcer. Thus he hasn't had to fight on a regular basis.
I think if these two ever came to blows, Scott would have the technical & experience edge to gain the win. However I don't think Chara would ever engage in battle with someone like Scott, it is a loss for his team, while Chicago would glady trade Scott's 5 minutes for Chara's.
Chara doesn't even try in fights. He knows what he can do to people, but at the sametime he knows what he means to his team. He'll get a few shots in wrestle someone down so he doesn't break his hand again. His balance really isnt that bad, he'd just prefer to end a fight as quick as possible.