I’d say it’s risky to retake a 515. You will likely see a gain in C/P but a few point drop in other sections, so it’s not worth the risk. However, your GPA is below the median for MD (and likely MD/PHD) matriculants, and your ECs look very solid for MD PHD. I’d recommend really crush your research year by getting as many pubs, abstracts, and conference presentation/awards as possible.