Programs know that every school has a different grading process. The dean of my school told us that they used to give people who failed a remediated a course a P*, but programs thought that meant HONORS. When we look at a transcript, we just look to see if they passed, and don't really care what they HP or honored, or how many courses. Board scores are much more of a level playing ground, but they are not with out fault either. A person can be a great test taker and terrible physician, and vise versa. And as far as your clerkship, you may have had someone grade you who was a little stricter, or that you didn't completely jive with. I think as long as you don't have a completely garbage app, and don't interview like a complete jackass, you will get an FM spot somewhere.