I've been having trouble in regards to faith lately, as well. I've only recently accepted Christian faith into my life - for the past ten years I've mostly been agnostic. Since I have done so I've been feeling a lot more confident in myself and have been noticing too many good signs - not just about my life but life in general - to ignore.
But not only am I struggling to decide if transition is okay but if it's even right for me. I was thinking about starting a thread about this but it's so closely related to this one and when it comes down to it, the answer is the same: Hold true to your faith, listen to your heart and find the answer from God through diligent, honest prayer. I can accept that being gay or trans (or both!) and remaining true to God are completely possible, but I've been having an incredibly hard time with my transition - trying to decide if I want to continue and fully transition, if I'm happy (and safe) where I am, or if I want to detransition, and continue to live my life as a woman. Axelle wrote something about this on the first page of the thread, about seeking answers when she was coming to terms with being trans and that the answer had just hit her one night and it was a do or die situation.
I'm a little terrified, to be honest. It's been over a year since I started going by Ryan and I'm getting cold feet. I have plans to do a lot of travelling and living abroad in a country (most likely Japan) where being gay sits on the edge of a knife when it comes to being acceptable, and where being trans and a foreigner could put me in a frightening situation if I end up in hospital or unfortunately end up convicted of a crime. I want nothing more than to make my father proud of me and while getting a full-time job, sticking to it, becoming financially stable and independent and basically growing up will greatly improve our relationship and his faith in me, I'm still terrified of losing him. He's the only parent I have left, and I also worry that my transition might damage his relationship with his girlfriend, and even the rest of the family.
I'm sorry this is so long. I'm not trying to distract from the original post and go off-topic. I guess my main point is that I, too am feeling conflicted about my faith in regards to transition and have been desperately seeking council from God. Maybe I should take a trip across town to the United church that's affiliated with Affirm United? Maybe speaking to the pastor about my situation will help? I've never been there before and haven't stepped inside a church since I went to a family wedding when I was 15. Even my mom's funeral was held at a funeral home as opposed to a traditional church.
tl;dr: I've been feeling kind of the same way, OP. I think having some sincere prayer sessions helps, as well as talking to a pastor at an LGBT-friendly church (in Canada we have AFFIRM United connected with the United Church - not sure about other countries though). If your family wants to have you speak with a Councillor of their choosing, tell them you've already been speaking with a clergy-person about your transition and have found peace with God about it.
thanks to everyone else who answered - it was helpful for me too!