I think the theory of weighting clinical grades highly is that, especially if you do well and work hard on rotations you are less interested in, then you will do the same in residency. So, following that logic, if some or a bunch of clerkship grades are less than stellar, some programs may see that as a reflection of work ethic. Probably does not apply at all to you or others in this situation. But, if you want to counteract that, the easiest way is to select away rotations at programs you think are a good personality fit and then be the hardest working best medical student they have ever seen. After interview day if any body brings up the clerkship grades, you'll have people on the committee that remember you or have notes from residents about your amazing work ethic over the course of an arduous month to counteract any potential critique.
Doesn't matter if you apply to 50 or 70 or 90 IMO. No one is particularly likely to get many interview from programs that are geographically different from where they grew up/went to school/did away rotations. Programs get too many applications, can't interview everyone, and want people who want to be at their program (not "just want to match somewhere"). If you are in the southeast, you are in good shape. If you are California born/raised/educated, it is more challenging. My sense, having been through 5-6 years of resident selection and my own application, is that good scores are assumed, geography matters, and the only way to take things into your own hands are to crush Step 1 and crush your away rotations. Can't change clerkship grades you got before, but if you are the best rotating medical student a place has ever seen and you seem like a good fit at a program, it goes a long way.
