Danielle-
I can understand your predicament. I had been in a very similar one years ago when I had to choose between re-applying vs. go D.O. Five years ago, the level of competition for M.D. medical school was at an all time high and anyone who had gone through that period will attest to that. This same surge of competition is also seen passing onto during the residency cycle. In my honest opinion, I don't really know how competitive the current market is for M.D. school, but your stats seem borderline at the moment if I had to compare it with how it was years ago (your stats are very similar to mine).
One problem I vaguely remember is that if you choose to retake the MCAT and if you also matriculate as a D.O. medical student, you are automatically disqualify to take the exam (you are no longer a qualify candidate). I ran into a similar problem years ago when my MCAT result would have been expired for the next application cycle. I knew that my borderline MCAT scores kept me from gaining acceptances or even getting interviews. I knew that I didn't have much room to play with being in such situation. I realized then that the MCAT was solely design to take money and make your life hell.
As for your other options with further post graduate studies like Ph.D's. or M.S., I honestly don't think the adcom at M.D. schools really care much for this (at least for me when I applied five years ago). I also have an M.S. degree from a prestigious institution (did very well), but the politics of the admission process will dictate who gets in. Getting a Ph.D. is great if you are planning to go into academics, but if your plan is to practice as a physician, I absolutely don't see what the purpose for this is.
About a third of my current D.O. classmates have Masters and Ph.D. degrees. A large proportion also have nursing, paramedic, therapist background. Two-third choose to go into M.D. residencies. The other one-third went into D.O. residencies, but all competitive ones like Orthopedic Surgery, EM, ENT, Optho, Derm, Urology, Radiology, Neuro. Surgery etc... Honestly, the only regret I had is spending so much money and time for a Master degree and re-applying while some of my college classmates who went D.O. are currently practicing as physicians making $200K+ in their jobs as attendings. Nothing is worst in your medical career than to find an intern or resident who in life know so much less than you, but in medicine knows so much more than you. The lesson I learned is beggars can't be choosers.
Hope that helps, good luck in your search for a spot!