This is a bad situation to be in. I had the same problem with my med school and basically wanted to ring the peoples' necks. I really think you need some clinical grades. I had people comment on my honors in surgery and internal medicine. One competetive program actually told me that they don't like to take people who don't honor surgery because they think it is a mark of work ethic or something. (This seemed stupid to me.) I would really try to get your school to post those grades because some programs won't really understand why they don't have your grades and may consider it a red flag (ie did you complete third year yet? did you fail roatations.) In any event I doubt any program will view it favorably. Good luck I know its not a good spot to be in.