Author has written 2 stories for Fullmetal Alchemist.
Link to the cover of Traces of Innocence (And all it's horribly colored goodness)
To clear some confusion:
In my FMA stories I am using the anime universe with my own twists. Mustang still killed Winry's parents and she hates him, despite Edward being married to him. (You read right. They're married.) Mustang is missing his left eye, thanks to Archer, but Archer is not an automail freak. I can't use him like that. If you read my fic "Traces of Innocence", you can find out more about what happens with Archer.
Edward is indeed a hermaphrodite. Meaning he has both genitals. Penis and vagina. Ovaries and all. But Edward doesn't feel he is a woman, despite having a child. The only reason he got the uterus is from the Gate. The Gate takes and gives. During his pregnancy with his son Maes Elric-Mustang, his body had generated a pseudo-vagina in order for the fetus to find a way out.
Alphonse has his body back, from the Philosopher's Stone, and is happily married to Winry. He lives in Resembool with her, and they run an automail shop.