Each school has a different system for grading. Before I can determine what your grades mean, I have to look at a couple things in your ERAS. First, I read any included blurbs provided by your school about how their grading scheme works. Second, I look at the included histogram of grade distributions in your class. I will know for each clerkship if only 5% of people get honors, or if 50% of people do. This is the most helpful part for me in terms of comparing candidates from different schools.
How much do comments from attendings matter? Depends on what they say. Most comments range from saying positive things to saying extremely positive things, so the comments really only give me any information if they are negative comments. That said, one negative comment won't sink your boat, as I understand you may every so often encounter an attending you don't mesh with. If your comments across multiple rotations point out the same deficiency though, then we may have a problem.
It's the things that set you apart from the pack, either positively or negatively, that will matter most in your app. For you specifically it sounds like the shelf grades will be most important, since they will determine your clerkship grades.
