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Well that's remarkable.  Did you follow some kind of program or just run?  Many people run for decades without really coming close to breaking 3 hours (I'm probably around 3:20-3:25 on my best day).  Whereas most university graduates could probably get a couple of first author publications if they made it a priority. Sadly I'm not sure non-runners on the admissions committees recognize this difference.

Personally I think your chances depend on your location.  If you are IP pretty much anywhere other than Ontario then I think you are in very good shape.  Make sure you get some realistic MMI practice if you haven't done that before.

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As far as your stats, this all looks very reasonable.

Curious, what was going on with your grades? It might be worthwhile to explain the fluctuation in applications, though you are obviously academically capable. Make sure when you ask for a reference letter you pose the question "Are you willing to write me a strong letter in support of my application to MD school". It would probably be helpful to provide your referee with a vague idea of what this might entail (i.e. a simplified version of CANMEDs roles, or Toronto clusters for Toronto). Since you are a more mature applicant, having referees that are longer standing would obviously be to your advantage (assuming they are all strong). With regards to the PHD, this is tricky. I would make sure you have a good rational reason for why you decided to leave, and (hopefully) it wasn't performance based. On the same note, you say you "KNOW" you want to be a physician....make sure you have strong evidence to back this up. It's hard to really know what medicine is about unless you've had some clinical exposure. I would focus on the specific skills or tasks you enjoy (and have had exposure to) that a physician might do that your PHD will not allow you to do. Don't approach it from the perspective that you KNOW you want to be a doctor. 

Not sure if that helps, but overall I think you're in good shape (sans red flags I don't know about etc).

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