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MD 2.9 GPA and 38 MCAT score. Retake classes, MCAT, special masters, or post-BAC?

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I just finished my junior year of college (majoring in Chemistry + Biology) with a 2.9 GPA and a 3.1 S. GPA, I have been on the Dean's list for that past year and a half. However, my grades from 2nd sem. freshmen yr and 1st sem. of sophomore yr is what's taking a toll on my GPA. My low GPA and a few W's are due to a combination of a medical illness and family issues. I couldn't do a complete withdrawal because financial aid would require me to be obtain a certain amount of credits per year (even if I was failing the classes). So, it was a choice between bad grades or being in debts.

I'm a first-generation applicant; neither one of my parents went to college, so I was greatly disadvantage in that sense. My family came to the US as refugees 6 years ago, I started my first year in High school here, and was able to graduate with a 3.9 GPA in under 3 years even though I had to overcome the language barrier. Both of my parents are janitors here, although they both had respectable jobs in my home country.
I've been volunteering since high school. I teach English to non-English speakers, and I also teach two other languages.

I have being doing research for two years now, and about to get my first paper published (2nd. author).

I only have a few months of clinical experience, and no leadership positions! :/

What should I do? Retake the MCAT and score in the 40+ and retake some courses? DO a special master? or Post-BAC? I'm also considering Teach for America for a year.

Any advice is appreciated! :)

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