For 'canon' purposes, why not make them both LSM? Since there are problems in both games which refer to them as he, just set it up as the 'canon' way of the story.
But that doesn't mean people can't enjoy the game with any gender/alignment. It's just the light side male thing seems to be 'canon' as far as the storytelling and dialogue problems go.
Oh, as for K3, forget forcing one alignment/gender to the previous characters. Have the quiz thing for people so they can enjoy the previous characters. Let everyone continue as they played the first two. A female player who did darkside is going to have NO idea what people are talking about, but of course set a 'canon' for the character.