Does soda actually make you shorter
like break down your bones a little

I actually don't believe it necessarily breaks down your bones, but science has proven that soda has managed to make your teeth decay faster in a way.

No i does not so far and their is no evidence that caffeine has any direct efecct on ur height 

The answer would be fracture.

Probably because you wake up early. even when i get a good nights sleep i still feel tired if i wake up early. or maybe you just need coffee.