Though running can release endorphins, it is also a natural treatment for depression. I lifted weights every day before I transitioned, and it never changed the way I felt about my body being not right. Perhaps the running is getting rid of the depression, the dysphoria. I don't know if it would change how you felt about the body you are currently in.
Besides talking to a counselor, keep a diary about how you feel from day to day, before and after running. Not just your emotions, but what you consider yourself to be. Male or female.
sam1234