I don't want to dash your hopes, but those numbers may be a bit on the low side for the better US MD-PhD programs. While an American with those credentials has a decent shot at mid-range programs and a chance at upper-tier ones, us foreigners are held to higher standards at most places (I'd say 3.7-3.8 GPA and 36 or so for the MCAT). On the other hand, though, you have two advantages: a very solid publication record and an advanced degree. I would certainly not rule out some adcoms overlooking the numbers given your strong research background. Also, you went to a school where high GPAs are very hard to come by, and those who are familiar with the rigor of U of T will take that into account.
There are a few options to ponder.
1) Apply to U.S. MD-PhD programs. Apply to all of the lower-tier ones from the list of schools accepting foreigners (of course, these are all above average schools), and a few reach schools, especially if they have particular faculty/programs you're interested in. I won't guarantee success, but you never know what will happen. If your current research supervisor can put you in touch with people at places you're interested in, that may work in your favor when you apply at those places.
2) Apply to U.S. MD programs. This doesn't sound favorable to you in light of how expensive US medical education is, but you will certainly have a shot at the lower-mid range schools, and again at a few reaches. Again, the $$$ involved doesn't make this a great option.
3) Think about staying in Canada. I know how competitive Canadian school admission is and again your GPA may be on the lower end of what places will consider but... the Master's is definitely to your advantage. Also, at many Ontario schools, graduate GPA is considered more heavily. Is that cGPA your undergrad or grad result? A strong master's showing can make a good impression for at least those schools and probably some other Canadian ones. Also, at many places, there is heavier weighting towards the upper years. If you've done better towards the end of your degree, this can work in your favor. Check with individual schools, but as I remember from when I was applying, there is greater leniency in general with graduate school work.
Also, the MCAT result, which is on the lower range of upper-tier US schools and is considered heavily by US adcoms, will not hurt you at most Canadian schools, since there you usually just have to clear a particular cutoff (which you will easily) and it's not counted very much from that point on.
Lastly, money. Apply MD/PhD at some places and if you want to be considered for MD only in case of MD/PhD rejection, let them know that too. In any case, funding or not, Canadian medical education is way cheaper, and if you want to work later on in the US, it seems pretty easy to get licensed there as a Canadian medical graduate (certainly easier than going back to Canada).
Again, PM me if I can help more, and I hope others who have been in this situation can chime in here. All of the above options can be tried simulatenously though it will cost you some in application fees (OMSAS - yikes!). Good luck!
