I’m not 100% sure that’s true 
but, I am sure that submitting 4s on APs will not be why you don’t get an offer.
For Harvard, be aware that their first criterion for transfers is “A clearly defined academic need to transfer”. Coming from UChic that is going to be a challenging case to make.
MIT is looking for students who “bring something unique and special to our community”, and that’s not just marketing talk: they mean it. They really do believe in making a good match.
So, my advice is to save your application fees for these two. I don’t fancy your (or anybody else’s) chances for Stanford, but it is the most aligned with your goals (at least, as they were last year), and I have the feeling that your ‘prestige goggles’ won’t let you focus on being a shining star where you are until you take your shot, even though imo that is the better way to get to where you want to go!