What is the difference between Co to je and Co je to? Just stress? Is one form more common than another?
Yes, just stress. They are interchangeable. See my comment to Shannon at https://forum.duolingo.com/comment/27148270/They-are-small-animals and several similar comments, but for the question they are pretty much the same.
You cannot use jak in this exercise. As Renardo_11 has pointed out, jak is an adverb generally meaning "how." Co is a pronoun generally meaning "what."
There is no Czech word “yak”, as “y” is not used in the Czech language, except for foreign names.
“Jak” is a comparative and interrogative adverb roughly equivalent to the English “how.” I now can't think of a situation where it would mean “what.”
Since “jak” is an adverb it is not normally used with být (to be); I think you would have to use the neuter form of the adjective, jaké: “jaké to je?” = what is it like? (Maybe my word order is wrong here, and “jaké je to” should be prefered.) But that does not mean that “jaké” means “what;” it means “what … like” or “like what.”