Hi Melanie,
I hope things went ok for you when your pastor visited.
Depending on the church, it's not an uncommon thing, particularly if your family is relatively new to the church. Some pastors are keen on getting to know the members of a congregation on a personal basis, particularly in a small family sized church.
Now for your concerns:
1. Regardless of what brand of Christianity, they will all agree that God is a loving God. He loves us all - look to Jesus, and see how he associated with the dregs of society - prostitutes, tax collectors, etc.
2. You seem worried about rejection by others from church, and avoid it these days. That is totally understandable. Remember that ultimately, it is your relationship with God that comes first, and that the way others treat you does not reflect what He thinks of you. Jesus himself was despised, rejected, and was nailed to a tree.
3. It is not for us to judge and condemn. Theologically speaking, in the eyes of God, one sin is no worse than another.
4. As far as being trans is concerned, the issue at hand is what is male and what is female theologically. You can debate that one till the cows come home.
Feel free to PM me questions regarding this. I don't claim to have all the answers, but I can certainly give you my perspective with living as a transgender Christian.