1. Correct, I was confusing genetics with biology. My updated stance shall be that sex is determined by our genes (excluding rare cases of intersex, I know).
2. I totally agree, but there is lot of evidence which shows that all other activities in our daily lives change our brains. My claim is not too far-fetched. There is also no evidence that these transgender males had female brains at birth.
3. This is actually a bad point. From your perspective it makes sense, but that is a subtle way of putting words in my mouth. By using that analogy you are assuming I also think gender is innate through our genes. If I woke up in a female body tomorrow, you are totally right, I would feel totally lost. However, I don;t think that people are born this way. I think it is a disorder and I also believe in the ability of people to convince themselves of anything. I think it is a natural part of human behavior.
While I disagree with your opinion I do respect your ability to defend yourself. It seems like that's not something a lot of people care to do.