If at any point the caramel separates from too high heat, just put it in a cold water bath and whisk it. It should come together when cool.
I always eat my s'mores with peanut butter, so I would suggest maybe adding some peanut butter to either the pudding or caramel if that sounds good to you. I realize that the majority of the world does not see peanut butter as an essential part of a s'more, so I tested this recipe the generic way.
Recipe updated 7/11/16