You won't like this.
AMCAS and AACOMAS open in what, 3 weeks? Your app is done for 2015-2016. Too late to do anything for this year.
If you're serious about applying this year then you need to get going on your DO assets. Hint: you need a DO letter.
Regardless, you shouldn't be trying for MD with your app as it stands. If you want MD, you need to improve every number. Your numbers are all 1-2 std devs below average for MD matriculants. With a math degree your physics section, at least, should shine, but it doesn't. There's no confidence-inspiring academic work in your app.
One year of meh in a terminal masters does nothing to help with the meh in your undergrad work and the meh in your MCAT.
In your shoes, if MD is what you want, I'd be looking at a rigorous traditional grad program in a hard science, and I'd be hellbent for pubs. I'd also be hellbent for a WAY above average MCAT. The plan would be to reapply in about 3 years. I'm totally serious. I have a math degree and came back from worse damage than you have.
I'm baffled as to how an "adcom" can give you extensive help on your PS, as if that matters with your numbers. As an "adcom" this person should have some comprehension of what a competitive app looks like, and should understand that an intense PS effort for MD schools is 2-3 years in the future for you.
Sorry you got bad guidance and wasted an app year.
Best of luck to you.