I think that the reason for the tornado could be that Danny had decided not to pay the money to his "friend", or at least that he wasn't doing the right thing with it (the money was stolen from his sister/father in the first place).
I think Danny and Larry's decision is meant to be sort of parallels, the story begins with them both having money in their hands, Danny, the $20 to pay for his weed, and Larry, the large amount possibly as a bribe. Then Danny gets his money taken away, the choice is no longer in his hands. Larry, while deciding what to do with the tainted money, experiences a downward spiral in every aspect of his life.
Then Danny goes through his Bar Miztvah, thus becoming a man, and the Rabbi gives him his radio back, and thus puts the decision back in his hands (and tells him to be a good boy). And now that he is an adult he can suffer consequences for his actions.
So in the final sequence we see Larry (after just receiving good news) decide to make the wrong decision and he is punished with the phone call. Then we see Danny looking down at the money and then at the guy he is supposed to pay back, and it appears as if maybe he was about to get his attention but maybe changed his mind. Did he also make the wrong decision?
Another sign that money could be tainted is that in the dream sequence Larry gives Arthur the money and Arthur is immediately shot in the neck.
I have read reviews where people imply that this film is about bad things happening for no reason, and that's what the Coens do. But I think in all their films bad things tend to happen to greedy people. The difference here is that Larry wasn't trying to be greedy. He didn't steal the money, he did do anything as he said, but he still chose to keep the money.
Or I'm wrong and it is a movie about how horrible things just happen.