With an undergrad GPA of <3.5, you are probably getting caught in the first pass filter and nobody even gets a look at the rest of your application.
I'm not totally sure how to remedy this. I think postbac programs will count toward your undergrad GPA but if you already did all your science prereqs I'm not sure you can take that route.
In your shoes I might try to think about alternative paths to the career you want, including starting with a straight PhD, for which you would be a much stronger candidate and could very reasonably expect to enter a great school in the geographic area of your choice, or else a straight MD (but you might need to consider casting a wider net in that case).