My overall GPA is 3.41 and my science GPA is 3.35, with a 34 on the MCAT (12 VR, 11 BS, 11 PS).
Your stats are fine if you were applying MD-only, but I don't know how competitive you'd be for MD/PhD.
The problem with sitting out a year is having go through the process of applying to grad school again in a year or so if I don't get into a MD/PHD program next year. Plus, I wasn't sure if completing my first year of classes in the doctoral program with above-average grades might compensate for my lower undergraduate GPA.
The only way getting good grades in grad school will help compensate for your UG GPA is if you do an SMP (special masters program). These are programs intended for people who have good MCAT scores and need some GPA rehabilitation. You take med school classes with the med students, and it's high risk, high reward. Doing well can help you get an in at the affiliated med school, and doing poorly may dig you a hole so deep that you won't ever be able to climb out of it. IMO, your GPA is too high to make it worth doing an SMP, at least for MD-only. I don't know how MD/PhD programs view SMPs, so I'll leave that for someone else to comment on if anyone knows.
I want to caution you that you should *not* go to grad school with the idea of using it as a stepping stone for med school, *especially* with the plan of dropping out in the middle of the program if you manage to get an MD acceptance. Adcoms prefer to have people complete their degrees--we don't want someone to get a year or two into med school and then skip out on us just like they did in grad school. Also, your PI may be rather unhappy with you if you bail early, and you need a LOR from him/her for your med school app. Burn that bridge at your peril.
Assuming you are sure you definitely want an MD, here are some realistic pathways you should consider:
1) Do a regular research MS, which would typically run anywhere from 1-3 years. Spend this time preparing to apply either MD-only or MD/PhD. Benefits are that you'd get some significant research experience and hopefully a strong research LOR from your PI. However, the MS may not take any time off your PhD, and you may not get funding. Definitely ask about that.
2) Take a glide year and use it to apply MD-only. Your stats are high enough that you should be reasonably competitive for MD programs, assuming you have good ECs, LORs, essays, etc. Once you get into medical school, you can add on a PhD if you want. It is *much* easier to go MD-to-PhD than it is to go PhD-to-MD. The downside of this is that part or all of your med school may not be paid for.
3) Complete your PhD and then apply to med school. This is what I did. While possible, it's probably the least desirable of the three paths I'm laying out here. Getting into med school doesn't get magically easier just because you have a PhD, and you will still need to do all of the same things (shadowing, etc.) that trad premeds have to do. Doing separate degrees adds a lot of time to your path. Also, you will almost certainly have to pay for your entire medical school.
If it were me, I'd apply both MD and MD/PhD this summer and find a job for this year, preferably in research. If I didn't get into MD/PhD but did get into MD, I'd look into transferring into the MD/PhD program once I got to med school.
