Sorry to disappoint you, but you did maybe ~25% of the work required to achieve a 90th percentile score on the MCAT.
Please take a deep look at the following threads:
Compilation - MCAT Study Plans and MCAT Study Strategies
509+ MCAT Study Habits
Some common denominators I have seen in high scoring individuals:
1. The usual review schedule was along the lines of 1/3 content review, 1/3 practice passages and review, 1/3 practice-full length. All study plans seem to be a derivative of the original SN2ed plan, modified to include Psych/Soc and new testing materials and changing FLs.
2. Study periods ranged from 1 month (recent retaker, content review finished, purely for practice passages and FLs) to 3 months (full time MCAT review) to 5 months (part time student/employment with MCAT review on side).
3. Most did NOT take a full course. This is either due to the cookie cutter approach being highly inefficient (ok for most, perfect for a few, useless for many) OR initiative/discipline to generate a tailored personal study schedule.
4. AAMC materials were an absolute must. Section banks completed with a 60-80% pass rate minimum, and completion of FL1, FL2, (and now FL3) in the weeks leading up to the exam (saved for last).
5. Other FLs used were generally NextStep or Altius. Limited success with Kaplan/TPR/EK.
6. Deep and thorough review of every practice passage and FL taken. This means reviewing both correct and incorrect questions, along with Q&A manipulation to encourage a deeper thought process and understanding of how questions are structured. Error logs strongly recommended.
That's all I have off the top of my head.
A good CARS score is encouraging. When I see lower science scores, but a higher CARS score, it tells me that your reading comprehension and test-taking strategies are strong. This leads me to believe this is a content review issue. Regarding your content review process, while taking detailed notes is great, you've made a critical error: approaching MCAT2015 like it is the old MCAT. What do I mean by that? The new, revamped MCAT, while still requiring a strong science background, no longer heavily emphasizes memorization and minutiae to achieve a high score. The emphasis is now on critical thinking and analysis utilizing high yield science principles. Additionally, the sections are now much less black/white. Before, you would never see physics and chemistry intermixed with biology and biochemistry, but now I would hazard a guess that the sections are more like 90% primary focus, 10% interdisciplinary focus. This means that 90% of your C/P section focuses on chemistry (general and organic) and physics, but 10% of the material tested would be biology- and biochemistry-related.
Recognize that the new MCAT is incompatible with the brute-force strategies of the old MCAT. Whereas before you could get away with 70% content review and 30% FL practice, you absolutely cannot now. You need to use the AAMC materials, as well as much more practice passages and a deeper review of your completed practice problems.
Specific advice: Your C/P score appears to be the biggest weakness. I recommend you utilize TBR for that. While TBR is highly recommended for most sections, Phys/Chem is their strongest area. Completing the entirety of the GChem, OChem, and Physics books offered by TBR, including the practice passages, should net you a 2-3 point bump in your C/P score, and perhaps a 1pt bump in your B/B score as well.
Using the AAMC section banks and FLs should also net you a 2-3 point overall score bump. Combined with the 3-4 from TBR, you should see an overall 5-7 pt increase, which should be enough to land you in the 510+ promised land that you seek. But this is only if you use the materials, and your time, correctly.
Remember, the score to effort ratio is non-linear. It is more logarithmic than anything, meaning as you score higher and higher, the work required to get that next point becomes greater and greater. 500 to 506 requires much less work than 506 to 512. Recognize that, embrace it, put in the grind, and you'll do well.
Best of luck!