Where did you do your undergrad?
You majored in Bioengineering, and to just find classes at other institutions to replace those classes will be tough at best. Most non-enrolled courses being offered are introductory with a few exceptions.
Also since I see you opted for WAMC for only MD so I'm guessing that you're not considering DO?
Your master's GPA is solid. That shows that you are able to handle upper-level medical courses just fine.
Take it from someone who was in an extremely similar situation (cGPA 2.7 sGPA 2.5).
Your number ONE priority right now is to rock your MCATs! Your success at the master's has shown that you can handle tough graduate coursework.
You'll need to beef up your extra-currics. What are they by the way? Have you any research experience? How about community service and volunteering? These are a close number two on your priority list.
My best advice is the following:
1. Study study study for the MCATs, from now until the next app cycle. Make this exam your life. Take your time. Know this exam inside-out.
2. Do research (paid if you can find it; paid/unpaid matters not in this regard) until the next app cycle, and get involved with community service while continuing to shadow. By the time you're ready for interviews, you'll have an entire year and a half of all of the above.
Your MD acceptance is likely at least a year and a half away (applying now without an MCAT or having studied for one should not even be considered), but I think that will be your best bet to improve your application.
Good luck