My rough figures suggest that you're at about 3.41 right now, and that after another year of 4.0 grades you could be at 3.55. Not too bad.
Since you got a higher grade in the second course of the OChem and Physics series, you don't HAVE to retake. But if you didn't understand the material well enough to do well on the MCAT, you should retake. You still need to redeem the negative effect those Cs had on your GPA and BCPM GPA, but getting As in other upper-level science classes will accomplish the same effect.
A traditional masters degree will not make you a better candidate for med school unless you need the opportunity it would offer to gain research and teaching experience. And you can get those other ways.