Your cGPA and sciGPA are fine. Your cGPA may be even closer to a 3.6 since AMCAS will count your community college courses.
Since you are a CA resident, you are going to make your application more competitive -- which is true for the majority of CA students, given the competitiveness there. Your advisor is probably harsh because of her experience with the medical school admissions process in CA. Nonetheless, I disagree with her comment that you have no shot for MD.
My advice:
1) Retake the MCAT. You must get at least a 30 to be considered competitive. A 30+ MCAT combined with your GPAs will make you a decent MD applicant. Look at the MCAT thread here on SDN for tips on how to score a 30+ on the MCAT.
2) While preparing for the MCAT and waiting to apply, spend this time working on your ECs. Make sure you have good clinical experience (volunteer or paid) and develop your hobbies or other interests. You need to stand out and to do this, you just simply need to pursue things you care about or are interested in. There is no magical EC checklist. Btw, I notice you do not have shadowing--you definitely need physician shadowing! Some of your experiences are interesting, and you should try to continue them if possible. Having long-term experience is beneficial because it shows commitment and you can talk about your experiences more meaningfully.
3) Only retake courses you got less than a C. If you need to retake a course, do not re-take them at a community college--it will be obvious to ADCOMS that you are taking the easy way out.
4) Your explanation for the 5 W's is perfectly acceptable. You can disclose this in your personal statement or on the secondaries that specifically ask you to explain academic discrepancies or problems.
5) If I were you, I would not do a post-bacc. I would definitely not do an SMP--these are last ditch efforts for med school. Your GPA is FINE--that is not a glaring weakness (your MCAT is). Taking additional advanced-level science courses may be beneficial to you, but I don't know if it will be worth it for you to bump your GPA from a 3.57 to a ~3.6 (at best). You are certainly free to do this, but think about how difficult it is taking courses and studying for the MCAT at the same time.
6) A masters degree or any graduate degree will not always help. If you are truly interested, then it's fine. But ADCOMs cannot compare applicants based on graduate work since the majority of applicants do not have graduate work.
7) Lastly, plan on applying to schools outside of CA (private and OOS-friendly). Apply broadly and early. You should be fine.