http://roygbiv.jezebel.com/the-next-top-doctor-in-pennsylvania-is-a-transgender-wo-1680606632
There are more transgender people in medicine than you think. Some of us figured out that the only way we could be completely assured of having competent, compassionate physicians for our community was to become those folks ourselves. I'm FTM, and I'm an MS-II also right now. I left a really good career to go to medical school at 37, because several doctors refused to provide care for me or for other trans people saying that they "just weren't comfortable" providing medical care for someone with our "issues." One in particular said that to someone I cared about and I kinda blew a gasket and registered the very next day to take the MCAT.
Pick your specialty based on your passion, and don't sell yourself short. Go do audition rotations at programs that you think that you would like to train at. Let them get a chance to meet you and work with you and see your work ethic and your potential, and your gender won't be the most important thing that they know about you. And with that in mind, I've found that if I don't make my gender a big deal, other people don't either. You mentioned that you "pass." That is a privilege that not everyone has, and yet it doesn't really matter that much. If you act like your gender history is something to be ashamed of, or that you need to hide, other people will be more likely to pick up on that and treat it the same way. If you move past it to focus on the things that matter, that is acquisition of a strong base of medical knowledge and genuine compassion, professionalism and total focus on the patient and doing the right thing for them... yeah, your gender becomes basically irrelevant. Medicine isn't about the doctor, after all, but about the patient. Keep your focus there and you cannot go wrong.
I've been at this (being gender variant) a bit longer than you, and I can tell you that a little humor goes a long way. One day, a fellow nurse teased me when I was running up the hallway. "Dude. You run like a girl!" I was like, golly, why do you think that might be? And we laughed it off... after he realized that I wasn't going to tear him to pieces or report him to HR. Even people who don't want to discriminate against us for religious or transphobic reasons, can still be uncomfortable around us because they are so afraid that they are going to screw up and say something / do something offensive. That makes them feel anxiety around us, and being a cause of someone's anxiety is a bad way to make them want to have you around. So, again, I say... the more chill you can be, the more you can put other people at ease in whatever way you find that works for you to do that, the less they will feel "uncomfortable" dealing with our "issues."
More urban is going to be easier than more rural, pretty much across the board. That has less to do with the physicians, who will likely have been drawn from all over the place, than with the hospital staff, who may have never lived anywhere but their one little podunk.
Right now, you need to be focusing on getting the best board scores that you can. You need to tear those exams up, just like any other student who wants to be competitive. I'm going FM all the way, because that is where I feel that I can do the most good for the communities that I want to serve. And I have some strong preferences about geography, etc. So, there are particular residencies that I want. I'm aiming for an 85th percentile board score for my first exam. Some would say that is overkill for FM, that I just need to pass. But it is always wise to be better than the minimum. And my high goal is achievable. It is just a matter of putting in the hours of study and staying keenly focused. If I do fall short by a few points, I'll still be in a much better situation than if I was just aiming to pass and only barely managed it.
Every time my motivations starts to flag or I feel like slacking off, I just recite to myself the names of the doctors who refused to provide basic medical care to me and to my loved ones. And I remember that they, and other bigots like them, aren't going away. Injustice doesn't just go away. It is driven out by the efforts of those who love fairness and human dignity. Keep something like that, some touchstone that imbues you with the energy you need to just keep going forward. Look to heroes and heroines, like Dr. Rachel Levine, like Dr. Nick Gorton, like Dr. Christine McGinn. Heck, write to them, reach out and tell them that they are inspirations and that you would appreciate their mentorship and support, if you need that. Just keep your spirits up and keep moving forward.
But yeah, what I'm doing is otherwise not really different than what any student is doing to prepare for residency. Research residencies. Seek to do rotations at the sites of the residencies you are most interested in. Go to conferences if possible in the specialty of interest to you and meet program directors. Do well on your exams. Be an exemplary student and member of your community so that you find yourself with people willing to go to bat for you. None of this is any different than any student should do. You will find your right place.
Edit: It should go without saying, but if I can be useful to you, or if you just want to connect with someone else who might get where you are coming from, hit me up. I'm not always fast to respond, but I will get back to you. You get that... especially with boards coming up. But I am doing this whole med school thing because I do genuinely care about other human beings and want to be helpful whenever I can. That is really a standing invite to anyone who needs it.