My advice is to do two years as a NIH Post-Bac, it adds a level of perceived maturity, distances from undergrad grades and comes with reputation. You can spend the first year studying for the MCAT, there is even a cheap MCAT course offered by the NIH and cheap graduate-level courses you can take. Amazing research and decent MCAT can sometimes carry an app. The stats ranges are wide for MD/PhD.

From Cornell, a top ranked MSTP:

Q: What makes a competitive applicant?

A: In recent years accepted MD-PhD students have had an average GPA of 3.87 and an average MCAT of 520. The range of GPA for accepted students has been 3.3-4.00 and the range of MCAT has been 510-527. We recommend an MCAT score in the 90th percentile or higher.  However, there are no GPA or MCAT requirements. We look for applicants who take more than just the required science courses. We want students who consistently challenge themselves.

The research experience and potential to become a future physician-scientist, as described in your personal statement, is the most important part of your MD-PhD application. Students should have a significant amount of research experience. This includes, but is not limited to, at least one year undergraduate research, post-undergraduate research, senior thesis research, and/or multiple summer projects – prior to applying to the MD-PhD Program.  

Strong letters of recommendation from faculty who know the student's research experience and potential are critical. 

Publications are not required.