Will universities still accept someone whose grades are shaky the 1st semester of their junior year but are all A's their 2nd semester?

You should be able to get into Upenn or Duke, but forget about Harvard and MIT they almost never let people in with shaky grades. Try several different schools that you would like to go to and that you think might accept you. I have heard of someone with a 2.8 average and got into Harvard because of his sport and community activities. Just try harder and try to bring it above a 3.0 and you should be fine.