My school isn't quite as rigid as yours with grading, but it still isn't easy to honor clerkships here. I was fortunate to honor most of my clerkships, but many of my friends weren't so lucky. They were jealous of students from many of the top 20 schools, where nearly everybody gets honors for showing up.
It's unfortunate that residencies place such a huge emphasis on clinical grades in selection of applicants for interviews, but they have to. Outside of doing an away at that program, it is the best proxy that programs have to judge your clinical performance. Same thing with AOA, it is indicative that you are a good student. When you have so many qualified applicants for a limited number of spots, the programs end up choosing arbitrary screening criteria to get their applications down to a reasonable number.
At this point, you can't worry about your grades because they are already set in stone. You should focus on things you can control, like where you rotate, how hard you work on those rotations, research projects to work on, how hard you study for Step 2CK, and who you ask for letters of recommendation. Your Step 1 score is great, and you have some nice research accomplishments, but you want to make sure you check off as many boxes as possible to give yourself the best shot to match well. Without AOA or many clinical honors, you might get screened out at the more competitive programs where you don't rotate. So if you really want a program, consider rotating there. At the same time, be realistic. Don't rotate at all top tier programs, because it is just too risky in today's applicant environment.
Good luck.
