If he sees himself as trans the best thing you can do for her is to help her seek a lgbt group for support and a therapist who specializes in dealing with lgbt teens/adults. She needs to be empowered as her gender. If she feels genderqueer make sure you use pronouns they are comfortable with. Also understand that if she feels like a female she deserves to be treated as one regardless of what she currently looks like.

The best thing is to lay off being physical. Your friend needs to feel confident as their gender and be around people who will support their growth. You can be apart of that growth. Just dont expect him to identify as a male if she believes she is in the wrong body.

If you go to a uni or community college there is usually some kind of gay-straight alliance.