James, you have a lot of valid questions. I've asked myself the same things over and over, I keep praying "God, just make me a girl, don't make me go through this." But then, God doesn't work like that. God himself doesn't put these things upon us, he isn't the type of person who sits up on his throne and makes us go through hard things to test us. God doesn't make bad things happen, bad things happen because the first man and woman screwed up. The difference between us and the first humans, however, is we have the saving grace of Christ.
Lets look at it like this. Something happened that caused us to become trans, whether medically, emotionally, who knows, science is still looking at us. We were born that way or we came into it. There we have the problem: We don't feel right in our birth gender. God doesn't fault you for that at all, and he definitely doesn't fault you for wanting to correct it. As long as we have faith, he'll make things work out for the better.
I've been through a ->-bleeped-<-storm this summer with anxiety, panic, depression, and finally the realization that I'm not a man, but a woman. Through it all, however, I kept praying, asking for guidance. I had fallen out of church, following God, it was prayer when I needed something, I was a Sunday christian. But then I started to feel him there again, and I know, because he is God, everything will come out right on the other side. God is going to use me whatever I decide to do to change myself, because what matters to him is what's inside.
If you're feeling God discarded you, get rid of that notion. He didn't discard the israelites back then, and that was before christ died for us. If you're feeling that God discarded you, that's satan talking. He wants you to focus on the negative so that you can't focus on the positive, you can't hear God.
Something that may help you, it helps me a lot, let God take control. If you start feeling like you've been discarded, just say "Hey, God, I can't shake these feelings, can you do it for me?" It's truly liberating because hey, he does it, he's happy to. And then after that, you can start listening for him, and he'll tell you what he has planned for you, and that you've not been discarded.
Hope that helps, and I hope I didn't ramble too much, haha, I just typed what I felt.