Good Luck with everything. The only thing I'd say you didn't mention is your clinical experiences, which really does count. Since you are more research oriented, apply to schools that really emphasis research.
yeah get some clinical stuff. and make sure you emphasize on your Personal statement perhaps, how you've improved academically. really sell yourself on that as best as you can, and make sure you do very well on the mcat.
also, i know you're reapplying and everything this year, but your gpa is just too low. schools really focus on the science gpa, and although you've shown improvement in your undegrad, and did well on those grad classes, you still need to keep improving your undergrad. an improving grade trend is helpful, but when your gpa is 3.1 it's kind of moot. so maybe you could take LOTS more undergrad science credits instead of taking grad classes that dont even go towards a grad degree (or do they? i don't know).
best of luck
PS. get lots of help on your personal statement and essays because your english needs a little bit of work before it becomes perfect.
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