Messed up Junior Year. What can I do?

The best thing you can do is to retune your college list. Vandy, JHU, Berkeley are all big reaches. Your scores and GPA are just not competitive enough unless you have a very very strong hook. Make sure you have some good safeties. Then focus on your essays and recommendations for your reaches knowing that your chances are less than 15%. If you get in great, if not move on.