Complex sentence: After the change in lifestyle, Megumi still has a problem with the transition from male to female where at first even as Megumi dresses as a girl, she still feels more like a boy, and feels more comfortable when around Makoto.
Split into simpler sentences: After the change in lifestyle, Megumi still has a problem with the transition from male to female. Even as Megumi dresses as a girl, she still feels more like a boy, and feels more comfortable when around Makoto.