Every medical school you ask advice from right now will give you a slightly different answer. Unless you are gung ho about one school, applying to many diverse schools is critical to maximize your chance of success. Even applying with a Ph.D., medical schools care about your undergraduate GPA and they care about it a lot. It's a well-known fact that graduate school GPA's are a little more subjective. However, unless you have a ton of C's or worse in the undergraduate sciences (coupled with your nice graduate school GPA) I would not recommend repeating undergraduate courses. I see a lot of posts on SDN recommending this and I've even heard some premed advisors recommend this but, honestly, as a Ph.D. applicant, If you can handle upper division science courses and you are well-published, there's nothing whatsoever to be gained from repeating chem 101, bio 101 etc. or doing more postbacc undergraduate classes. It's lunacy and I'll justify this statement in the next paragraph.
I have several friends who did an M.D. after their Ph.D. Of those friends with undergraduate GPA's between 3.0 and 3.3, a fine MCAT performance coupled with publications is how they sold themselves. It's true that many schools screen heavily on the undergraduate GPA (especially state schools) and some of them even use a computer program to do this so they won't even see that fact that you've distinguished yourself as a research scholar. Expect to be screened out by many of those schools, so you must apply widely. If you are in communication with only one medical school that you are dying to attend, you pretty much have to do what they ask and you can ignore my advice which is intended for the general Ph.D. applicant with a couple of red flags in their application. To increase your chances, I would still apply widely anyway. I know too many people who have been 'promised' things by admissions ccommittees before application only to be devastated if things did not go as they expected. In the and, an offer of admission is a committee decision.
If you sell yourself tastefully, you can get into medical school. Expect to be taken more seriously by research-oriented schools who will anticipate your career goal of being a clinician-scientist and they may recognize your research accomplishments a little better. It's a well-known fact by people who have taken this route that an applicant with a very 'average' GPA and/or MCAT is more likely to get into a private medical school because they can admit whomever they please. Note: I am not implying that private medical schools have uniformly lower standards. Private medical schools make so much money from RO1's and tuition etc. and, unlike state schools that are mandated to pump out x number of doctors per year (so they're not going to chance you flunking out), private schools don't work that way. Much like QofQuimica, I did not have an undergraduate GPA and, unlike QofQuimica, my MCAT performance was pretty mediocre so I know I was screened out by some schools right away. I expected it and so I didn't take it personally. With a good graduate school GPA and several high-impact publications, guess which schools took me most seriously as a Ph.D. applicant to medical school?.....the higher-ranked private schools. I didnt believe it when I was told to expect this before I applied, but thats exactly what I experienced.
You can't change your past so don't punish yourself. Take as many graduate courses as your school will allow and do well in them. Study for the MCAT like your life depended on it and try to scoop up as many publications and awards as you can during your Ph.D. Also be aware that all medical schools will want to see sustained evidence of health care experience and exposure so you know what youre getting yourself into. In the end, a Ph.D. is just a piece of paper that demsonstrates perseverance and the training in medical school requires very different intellectual and personal traits. This is the best way you can market yourself. If I can get in, you can too. Lastly, be careful what you wish for: you might just get it!
Good luck!