This may just be your lot in life. I had a hell of a time getting over 88% in basically all the big classes first year. I'm probably going to be a B average doctor. But I'll be a B average doctor with a boat.
In all seriousness though, it sounds like you're learning the material rather than cramming and regurgitating. Cramming and regurgitating may be good for school exams early on (trust me, it's all I did first year), but actually LEARNING it will benefit you greatly down the road, especially in your later courses. If you really REALLY need to break into that A range, spend only the necessary amount of time required on the high yield info and try and shove some more minutiae into your brain. The minutiae, at least at my school, is what generally separates 88% from 92%.
Or you could just embrace the dark side, get more B's, do average or better on boards (USMLE especially) and be flexible with your residency location. Trust me, it's a lot less stressful over here.