Hopefully you're not expecting to apply this year. Your MCAT exam date is too late for this year, even if your other stats were strong.
Unfortunately even if you break 35, you're still missing the academic performance asset that med schools need to see to feel confident in you. Success and pubs in a PhD program can be assumed to get you past low GPA screens, but that low undergrad GPA is going to sink you when ~90% of the candidates have to get thrown overboard after interviews.
For better or worse, your undergrad academic performance predicts your academic success in med school, but your grad work does not. The ability to memorize large piles of simple content and then take multiple choice exams has to be demonstrated for med school. You may have demonstrated incredible focus and competence as a grad student, along with other great characteristics, but unfortunately that's not enough to get into med school, and more importantly, med schools have no way to evaluate your grad work. Adcoms aren't going to look at your pubs to see whether your journals are well-respected or not, unless you get incredibly lucky and one of your adcoms is a former biophysicist.
A very structured grueling SMP might help you. I say "might" because your undergrad GPAs are still front and center on your app, regardless of your MCAT or SMP score.
More undergrad would definitely help you, but you'd need to do 2+ full time years of additional undergrad to break through your cumulative GPAs. I doubt you're willing to do that after a PhD.
What I'd recommend is:
0. Get a clinical volunteering gig, 4 hrs/wk, and keep doing it forever. Show me you're willing to clean stretchers and do menial labor just for the privilege of being in a clinical environment.
1. Use this next academic year to build a respectable stockpile of fresh undergrad A's in hard classes like biochem, micro, neurosci etc. I'd say at least 4 classes, so you're doing 2 per semester, presumably on top of a job. If I'm your adcom I want you to show me that you're respectful of the med school admissions process by ponying up more undergrad effort to help me evaluate you against 40 billion squeaky-clean eager premeds who have never failed to succeed academically.
2. Use your September '14 MCAT score to get into a strong SMP that starts August '15.
3. Apply June '16 for best results. Or, be impatient and apply June '15 pending your SMP results to get in "somewhere".
Usually people hate this advice.
Best of luck to you.