From what you said, it looks like things will eventually unfold. She probably knows how you feel about her, and it sound like she is comfortable at least with it. Who know...
I had a crush on a girl 6 years ago, long before I even knew the word "transgender". We used to chat a lot. Hours, until sunrise. We chatted on facebook, so we only knew each other by photos. We always said "we should meet at a café or something, to meet face to face and have a nice talk. It never happened. Probably because we knew that would lead to something happening, and we both had our own partners at that time. ALso I couldn't even conceive she having any interest on me.
We weren't so close as you and your friend, but we've been together for more than a year by now. And I couldn't be happier. Unexpected things DO happen.