If Yale said no, I expect they mean no, as they didn't also say that special circumstances will be considered. Are you aware that Yale doesn't accept AP credits unless they are supplemented with additional higher level classwork in the same discipline?
I'd say move on and aim for other med schools. Q of Quimica, a moderator in the Nontraditional Forum, has posted there about how she got accepted despite going to a college that didn't give grades. Track that down and see how she did it. Also meet with your advisor; surely your school has grads that have gotten into med school and the advisor can fill you in on how they did it without a GPA. Well, actually you do have a GPA, and you may need to mend it some with classes taken elsewhere.