I was really hoping this semester would bolster my GPA, I am sorely disappointed that it did not. I have :

Physics II: B+

O Chem Lab II: B+

O Chem II: B+

Overall Science GPA: 3.47

Overall GPA(from previous pro degree): 3.63

I only have Bio II remaining this summer. I am prepping for the MCAT late this summer.

What should be the best course of action here?

You are behind the curve in time and a bit in GPA. Personally, I am not a big fan of having students take a late MCAT and applying late in the cycle. You may want to consider pushing back a year and bolster your GPA and prep to make a killing on the MCAT. Taking an additional upper level bio course or two, adding more volunteer, working in the field, etc would help.

The risk in taking at the MCAT late and applying late, if you score low, do you withdraw? Or do you proceed with a weaker application late in the cycle that a higher chance of rejection that will then flag your next application. The question I always ask students is your goal to get into medical school, or to get into medical school quickly?