One big challenge could be in the area of relationships. If she was in a romantic relationship as a girl, her partner may not be able to handle the change. Also, making new friends as a man can be difficult as she has to learn new social cues and behaviors that are associated with men. Socially, she may face discrimination or misunderstanding from those who don't understand what she has gone through.
The girl - turned - man may face challenges in terms of self - identity. She has to re - evaluate who she is now. There are physical challenges too, like getting used to a new body shape and strength. In the workplace, she may face biases. For example, if she was in a female - dominated field before, now as a man she may be treated differently. And if she tries to enter a male - dominated field, she may face resistance from those who are not used to having a 'former girl' in their midst.