In Australia you are fully protected by law. Your name change, gender change etc does not affect legal guardianship at all. That is not to say your wife may not use it in a divorce process or custody to get at you if that is what you fear. But I think legally that is dead in the ground.
The name change is very easy just go to google and look for Australian name change, it takes a few weeks to get the documents back.
Your therapist can give you the letters to change your gender on all legal documents including passport, medicare, ATO etc. The letter just says that Emily gender identity is female, she has had counselling and her documentation should be rectified to correctly gender ID her, it is a 'form' letter.
Just remember to carry a copy of your name change certificate for changing bank account name and that sort of thing, utilities want to see proof of name change they just need to sight it. I had a funny few moment trying to deposit an ATO refund into my account as it was made out to former name. Bank attendant was certain that I wasn't him and I agreed, but I used to be, we had a few good laughs about it.
The only sticking point is the marriage certificate. I'm female on every single legal document but since same sex marriage is illegal here I can't change that - Mmm High court challenge is just waiting for that one. It is just about country to the Federal Act passed in 2013 for not being able to change name and gender on the marriage certificate.
