Edit: A teenage boy transforms into a girl overnight when he meets his soulmate. He must find a solution to live with her again meanwhile she turns into a boy.

One cool plot twist could be, they are never boy and girl at the same time. So they must have a baby to be the savior the world, but every time they are ready, they are either both boys or both girls.

If you say the baby is to be the savior of the world, then you should tell us what the earth is to be saved from.

Set in post-apocalyptic period: As a key to human-race survival, two troubled hermaphrodites must conceive a child. Problems arise as the apocalyptic creatures seek the same (or the child or them).

The last apocalyptic creatures can be replaced with your antagonists. But if this helps.
I think the 'falling in love' thing can be the part of the bigger picture, hence did not mention.