Ok, a 506 on your MCAT for your current position is pretty decent, but I would hold off on taking the test until you're a bit more prepared. You really don't want to take the MCAT more than once, both for strength of application and your own sanity.
I believe you're going to need both some DIY post-bacc as well as a master's program to really maximize your chances. Since you have good grades otherwise, it doesn't seem like motivation or study habits are a problem for you (which is great). That means you need to improve your mastery of the concepts that are taught in your pre-reqs. I'd argue that you should retake anything you scored a C or lower in AND absolutely take biochem. Biology/biochem is an entire section on the MCAT, so that's an absolute must before you take the test. You don't need to take physiology again since that's not a requirement for most med schools.
I believe the 3.0 GPA cutoff applies only to your overall GPA and not any individual aspect (this is a general rule for most graduate programs). However, even with a sub-3.0 uGPA, I received an exemption into my SMP. So that's not something I'd worry about. You'll need to take the MCAT before you do an SMP, and I'd try to score in the 510 range (but obviously more is better). My SMP encouraged students to retake the MCAT after the program IF they scored less than a 510. This is because their knowledge and study habits improved significantly through the year and would be reflected in generally better MCAT scores.
Good luck, and feel free to reach out if you need anything
