At the risk of just being a little blog-whore, I was just thinking about some of these things. Rather than do a lengthy cut and paste and fix all the links, I'll just link to the original
post.
The thing to remember is that God doesn't hate you, bad things happen to people for all kinds of reasons. I don't think any of us can say why we're trans, but I think it seems pretty plain that God's not in the habit of making us happy cisgender people. Maybe he just really likes diversity.
I think the important thing to realize is that if you love God and love your neighbor, you're doing the things you need to be doing.
Every once in a while I feel the same way: what am I doing, can this possibly be right? We do what we can with what we have, and if we mess up, then hopefully God will have mercy on us. We're already banking on that fact, aren't we? Why should he be merciful about one thing and completely non-understanding and non-accepting about another?
I used to have a lot of trouble with the Old Testament laws, but the thing is, those laws are intended for Jews living in Israel. That's why today people eat shrimp and wear cotton/poly blended clothing. The laws and rules of the Old Testament weren't designed to make us feel bad, they were designed to sanctify the Jews from the people around them. The early church decided that gentile Christians didn't need to follow every letter of the law, only the spirit:
Love the Lord your God with all of your heart, mind, soul and strength. This is the first and greatest commandment. And the second is like unto it: you shall love your neighbor as yourself. On these two commandments hang all the law and the prophets.
I hope you find the peace you're looking for.