When I talked to adcoms after my first go round at med school, most of them told me (3.3 overall and 3.0 science 30Q MCAT) that the only thing i could do for myself was to retake the few science classes that I did poorly in in undergrad. Basically they told me that taking different classes (even if they were upper level science) would not tell them that I could do well in the types of science classes that they were using to standardize all the applicants (Gen Chem, Orgo, Phys, Genetics, Mol/Dev Bio). They also said that those classes were good predictors of how you would do in med school (God, I hope not) - unless of course you have a huge desparity between your science GPA and your MCAT.....which of course I did. Now mind you these were allopathic programs and I only retook ONE science class that I got a C- in before applying to D.O. programs and I was admitted to 3 D.O. programs this year.
I would definitely advise you to retake those classes that you did not do well in, as you will need those for doing well on the MCAT. As others have said, it will also be the quickest and easiest way to raise your GPA for D.O. since they replace grades. Even with raising your GPA, you're still going to need to do well on the MCAT (see my stats) to compensate for the below 3.2 science GPA. I would say that most D.O. programs average stats are 3.3-3.4 overall and about the same, maybe a little lower for the science GPA. MCATs are normally around 25-27 per school.