there are pros and cons to both for your questions; i'll discuss them briefly
basic science - yeah, it does look better in general. but it takes a lot longer to complete, and, in my opinion, and i'm sure others as well, its downright boring.
now, how would you compare one basic science publication vs. two clinical research articles? it's hard to say. with clinical you really get the volume. with basic, if youre lucky and the data works out and youre published in time; great. both have strengths and weaknesses.
home school - you get to work with them for three full years. you get to work on projects with them closely, and you'll get some great reccs hopefully. at where you go, you begin touching base with the guys there, always a plus.
HOWEVER, it is far more beneficial, in my opinion, to do a sub-I your fourth year at the school of your choice, do extremely well, and get a letter from there. unless you can work with your target school closely for the next three years doing research and sub-I there, then go for it. otherwise, i'm not sure how much a summer research project would dazzle them compared to an awesome sub-I where you really prove your work ethic, skills, and attitude.
hope this helped