I'm not a PD, of course, but as a person with a couple of red flags of my own? I suppose the good news is that your 99/99 scores could well be enough in vacuo to get you some interviews... you can deal with the ancillary crap in your personal statement. You will want to be able to show exactly what you have done to manage the situation and fix it. Frankly, I would imagine that you could probably apply for both OBGYN and Transitional Year, rank all of your OBGYN interviews first and Transitional Year interviews second, and then see where you land.
You are in a far better situation than many people, thanks to your Step performance. If you can show people how you have overcome your personal challenges, my feeling is that you still have a shot.
BA - Oregon ° MS - BYU ° MD - MU-Sofia
"When I haven't any blue... I use red."
- Pablo Picasso