Liquid magma,
As you have shared more information about yourself with us, it has become clear to me that you have performed admirably in medical school. For that, you should certainly be congratulated.
Just remember that the USMLE step 1 score is just one factor, not the only factor IM residency program directors find useful in their decision-making process. While some programs do use a certain USMLE score as a cutoff, many others do not. I certainly hope that UCSF and Harvard are in the latter group. Of course, unless someone in the know responds to this discussion, it will be difficult to say one way or the other.
Although your IM director mentioned that these programs would not even look at your application, I certainly wouldn't let that stop you from an all out effort to secure a position at these programs. You should ask yourself why the IM director made such a statement. Does he or she have some specific information to base such a statement on? It's not common for residency programs to share their screening criteria (at least the specifics) with other programs.
Lara also makes a good point. There are many other residency programs in these two cities that are well regarded. Having said that, at this point in time, you seem to have your heart set on one of these two programs so we should focus our efforts on maximizing your chances to obtain a position there.
I believe you should take things one step at a time. At this point, your goal is to secure an interview. To secure an interview, program directors will look at your board score, third-year clerkship evaluations, Dean's letter, letters of recommendation, and personal statements. You should do everything you can to strengthen these components of your applications.
A lot can be accomplished in the next four to five months before you send out your applications. Make inquiries at your medical school - seek out faculty who used to be on staff at Harvard or UCSF as well as those who are prominent figures in their field. Consider doing a rotation with one of them to help you secure an excellent letter of recommendation. As I mentioned in my previous post, a phone call from one of these individuals on your behalf can do wonders for an application. Don't underestimate the power of connections.
You can, of course, do an away rotation at UCSF or Harvard. If you choose to do so, you need to get started early because spots fill up quickly. With some research, you may be able to find out who is on the residency selection committee at these institutions. Perhaps you can arrange to do a rotation under the supervision of one of these faculty members. If your performance is impressive, believe me, the attending will share that with the rest of the committee.
In summary, your efforts right now should focus on securing an interview. After all, the fact remains that you can't match into a program without being offered an interview. Once you get to the interview stage, you will have the chance to show them why they need to rank you highly.
Good luck to you,
Samir Desai, MD
Assistant Professor of Medicine
Baylor College of Medicine