1 and 2 are definitely unnatural sounding, and number 2 especially. Number 1, I could imagine someone saying in rare circumstances, although it would still sound stiff and overly formal, but never number 2.
I believe the reason is because the first thing after "why haven't you..." is the most important part of the sentence, and the focus. In general, in this situation, the focus should be on the "checking the tires" part, so it has to come first. It would be an unusual circumstance for the time ("yet") to be the focus of the sentence. In the very rare circumstance that the time should be the focus, it has to be "not yet", because the collusion of "not yet" would be the reason you are upset. Separating the "not" out into "haven't", and then putting an extraneous word ("you") in between completely kills any reason for saying this sentence.