My application is also full of potential problems I did not mention. No research or pubs, for example. I've also had to take time off from school. The only thing I've done well on is my USMLE really.
Residency application is a stressful process so your anxiety is understandable. You seem to be polling about every different board on SDN. Although trends and rules tend to help with general med school application, residency is so much more individualistic that few will have your unique situation (good school but few honors, good step scores, but year-out with little to show for it). Therefore I don't know how much definitive help the SDN community will give you.
Do you have ANY OBGYN attendings who you can sit down with and be frank? Didn't you have to sit with your OBGYN chair for a letter? Did you run your application list by them?
At the end of the day, the only way to find out if you're eligible for top programs like Brigham/MGH and UCSF is by applying, interviewing, and ranking. Match day will be a surprise for all of us. Therefore the best you can do (much like everyone) is apply broadly and hope for the best.
PS don't refer to your school as "prestigious." It's a little gauche.