Not only that but there would have to be so many miraculous changes at the same time in DNA and EVERY SINGLE cell in the body for this to happen. And they would have to find mates in which these miraculous mutations could propagate in.
Making changes in every single cell of a body is what germ cells do on the regular. That's not a miracle, that's just sex. Although I guess it is a miracle that some people are able to have sex.
Well no. You've never read On Origin of the Species, have you? That not at all how it works. The theory is that nature works in a manner similar to a person who breeds livestock or flowers, choosing individuals to breed that have desirable features and culling the rest. Of the course of many, many generations, those with the most favorable genes for survival remain. Natural selection vs. deliberate breeding.
It's just a theory.