Quote: The breath is too loud and almost sounds kind of "out of phase" sometimes
If you hear too much breath try to put the microphone further.
I think I understand your "out of phase" trouble, flutes are instruments with few harmonics so they're very sensible to acoustic problems. In some stereo recording the flute seems to move at a different place depending on the note played, the F can be heard from the left, C on the center and A from the right.
Don't hesitate to spend time to place your mic, and to choose a good room and the place of the musician in this room.