If I am going to do Internal Medicine, is it ok for me to get my surgery clerkship director/professor to write me a letter? He will write me a great letter and I would like to use him.
Absolutely no problem. You should have one "department/chair" letter (if available -- not all schools do this), which is usually based upon your 3rd year rotation and 4th year sub-I. You should have one letter from someone you worked with on your Sub-I. The other two letters are open and can be from anyone you worked with. A good l;etter from someone outside of IM is a strength -- shows that you "play well with others".