Personally I think your background probably does make you a better MD/PhD applicant than a MD only applicant. With all those publications, and ideally great recommentdations from top PI's you stand a better chance with MD/PhD committees. Although you still need enough clinical experience to really be able to explain why you want MD/PhD, and not just a PhD. I think your GPA isnt too bad, especially with the upward trend and so long as you explain it somwhere in your application. I might be a little worried about the MCAT, especially if you want to get into the top programs. You should consider retaking it this summer if you plan on reapplying. Getting a 33+ will probably make a big difference. I Hope that helps.
