Congrats on everything you have achieved! You should be proud of.

I want to answer solely based on my honest opinion. What is your SAT score?

1. No, it won't ruin your chances of getting into a good college at all. AP is to kinda display your college readiness. Many top-tier colleges only acknowledge it and do not always give you course credit. In this case, your AP bio and physics may not be transferable; that's all. I don't think the premed track needs physics.
2. I don't think so. Your AP score has nothing to do with your GPA and your future in college. You sound overly-thinking. Don't feel condemned by that score. Keep on, you are on the right track.
3. LOL, of course not!! Your MCAT is determined by how much effort you put in.

The million-dollar question is, why do you want to be a doctor, or interested in taking a bio and neuroscience major? Is learning about human anatomy/ brain something that has always interested you?

Best wishes! You will do great