Switching between he and she

I am working on a story that has the main character one year into transition MtF. Is it wrong or less confusing to always refer to her gender as her? Example would be in discussing a flash back when the character was twelve. He often went with his father on weekend hunting trips. Or, she often went with her father on weekend hunting trips. When in fact at twelve the character was trying to be the son his father wanted while struggling and denying who she really was.

In my mind, I should always refer to her as female. That was my plan. I am running into situations were there is past interactions between family members and they are interacting with a son or brother. The father would say, "That's my son". The sister would say, "He's a good brother".

The story structure and outline is laced with flashbacks. To add to the complication, I didn't want to start out stating the main character is in transition. I want the reader to read about a female character. Only later, when love is involved, does the subject come up.

Have you all run into this conundrum? Any advice would be appreciated.