Kaylee,
My personal observation is that things seem certain when people who are in positions of authority such as pastors are there telling others what is certain. Such as this action and this action plus this and that belief = salvation. This action or that action = sin and damnation.
My belief is that it is God's judgment of me that matters; not the judgment of another human; my relationship with God that brings salvation or possible damnation. My belief is that the certainty God presents to us is unconditional love.
What is not at all certain is what God's plans for us are, how other humans' actions or interactions or even our own will affect those plans God may have for us.
I am certain that my questions and uncertainty about being transgender are caused by the feelings and opinions of other humans; my own family and society at large. That uncertainty can be very painful for me and I can tell that it is for you as well, however it is so very important for each of us to go through that uncertainty in order to feel absolutely right with such an enormous life altering epiphany. Not even necessarily in terms of God, but for us and our lives here on earth.
However, even trying to be right with God, we are bound to have doubts and second thoughts. Having true faith in God means having doubts as well. Does being transgender mean to you only bodily, earthly pleasure or does it mean feeling really right, true and who you are meant to be? In my journey during times I didn't even know I was on a journey, there was a certain amount of 'earthly pleasure' associated with my feelings. My 'epiphany' came, however, not out of any earthly pleasure but out of a realization of who I am and who I was meant to be. With that realization came a lifting of weight from my shoulders; a feeling of happiness I'm not sure I've ever known; a feeling of being right with myself and a love for myself which is necessary before we can love God and others fully.
For atheists, agnostics, etc reading this, I apologize for offense you may feel. I do not at all intend this as an absolute statement that has meaning for you or others with varying degrees of faith or none at all. Even for very religious, faithful people, I fully realize that what I've said may or may not have meaning for you. It does seem to me that putting God into the picture or not, our doubts are a healthy reaction for us in the long run in order for us to be absolutely sure we are who we believe we are. The process of self-doubt may not be necessary at all for those who know their gender from early childhood, though I think it may well be helpful for those of us who come to realize our identity later in life.
I've prayed, doubted, questioned over and over until I have no doubts left. This only leaves me sure and confident as I proceed from here. I've had only one meeting so far with a gender therapist but I welcome this time with her to further strengthen and complete my knowledge of myself as a woman.
Kaylee and Coolsummer, I can't tell you what God thinks, but from what I've read in your posts, you are who you think you are and if that is so, God certainly loves you and will only share in the joy of that understanding.