|In Hourou Musuko the protagonist is a boy who wants to be a girl who makes friends with a girl who wants to be a boy- and their character growth. It doesn't have any real conflict in the story and is a little TOO laid back, bordering on boring... But its the only thing I can think of that kinda fits.
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The female lead drifts away from crossdressing and wanting to be a boy so the story probably might not work for you.