I read this post a while ago, and I feel sorry that such a story hasn't received any replies yet. Maybe it has to do with the disconnect people feel because they can't relate to the subject matter. But I guess I shouldn't allow that to be an excuse because I think it is an excellent story.
Though the closest I can come to a relation is a friend of mine who feels similarly to you, a boy trapped in a girl's body, I feel that your story is an important one that should be considered. There is such a disconnect between religion and people who are transgender and homosexual. "Didn't your god make me this way?", the argument goes. Shouldn't people who have committed no crime other than being born differently be as accepted into this community as "normal" people? I think that this is one of the great crimes of fundamentalist religious thought, the criminalization or perceived immorality of people who have no control over these things: "born sick, and commanded to be made well..." so to say.
I also do agree with your refusal to attend your parents' religious services. Even though they may simply ask you to attend to humor them, your refusal is still justified because of the way that these beliefs have abused your psyche and how they condemn you for who you are and what you cannot change (might as well be racism, homophobia, or sexism in my book).
I'm sorry if this post is poorly written, I suck at writing, but I hope you find my thoughts worthy.
Be so very proud of yourself - I want to give you a hug. You will find that all religions are scared of sex, are hypocritical about sex, and that probably many of them also like to wear women's clothing, but just don't have the guts to come out.
So Atheism is the place to be. You just keep on finding out who you are, what makes you tick, that there are millions of people in the world the same as you. Be proud - if people love you, truly love you, they will accept you for who are are, if not fuck off. Find like minded people if you can - talk to more people on this site.
Many gay, bi, transgenders get married and have children, but most of them are hiding who they are - always be honest about who you are, and don't rush things. That's the mother talking now. lol
There is a site for Gay, Lesbian and Bi-sexual people. I bet there are also Transgenders there.