I'm sorry if I sound uncaring or cruel Shawn - I totally don't mean to - but you have GOT to separate your religious and gender issues.
Think of it as a personal separation of Church and State.
On the one hand you are a person who believes in God.
On the other hand you are a person who is in great pain, trying to come to terms with the reality of their gender identity.
I can imagine all sorts of ways in which a belief in God's love, for all creatures, would be a comfort. But when other people's interpretation of God, and their bigotry and intolerance become a hindrance to your search for personal identity, then, honey, you just have to tell yourself: 'This isn't helping me. This is hurting me. I don't need this sh*t.'
Only you know who you are, what you are and how you feel. A therapist can help you with that. A doctor can help you. A surgeon can help you ... But some idiotic pseudo-priest who thinks that communion wine represents sexuality - and, BTW, show me the Biblical justification for THAT - absolutely cannot help you.