Also, I am in the Math Team, Debate Club, and Academic Decathlon. Although I am not doing very well in those clubs, are they going to help me for getting in MIT?
First the good news: An A- in any freshman class, especially physics (not usually a 9th-grade subject) will not hurt you at MIT, Harvard, or anywhere else. For starters, colleges look only at final grades and not those from each marking period. And even a final grade of A- will have no impact on your college prospects.
As for the extracurricular activities you’ve chosen, these all suggest that you are a serious student—the type whom MIT seeks.
Now for the bad news: The clubs you’ve mentioned (Math Team, Debate Club, and Academic Decathlon) are all extremely common on MIT applications. I could see an admission officer falling asleep before even getting through your list. 😉 So, if you want to stand out in the extremely selective MIT applicant pool, you should aim to move beyond the standard high school clubs and do something more memorable … perhaps outside of school … such as a research project. Admittedly, it can be hard for a teenager to conduct research independently but, if you can come up with a great idea, you may be able to enlist a professor at a local college to back you. Even one of your high school science or math teachers might be willing to support your efforts. Since you’ve said that you’re not “doing well” in your clubs, you ought to look further to come up with a more unusual–and perhaps more satisfying—activity. Sure, MIT does accept candidates whose résumés include only school-based organizations and no outside endeavors. But if MIT acceptance is your goal, you’d certainly improve your chances by pursuing a path that highlights your uniqueness as well as your brilliance.