1) You can certainly use a sky goddess and an earth god if that's what your pantheon has to offer.
2) I don't recommend using one deity of a pair without the other. On the other hand...
3) You don't have to gender the elemental deities, or any of the deities, in the ritual -- keep in mind that Christians and Jews use the SoP, and they've only got one divine gender to work with! If I were doing the SoP in a Shinto concept I'd certainly assign Inari to the north, the direction of earth.
Re: Shinto SOP
2) I don't recommend using one deity of a pair without the other. On the other hand...
3) You don't have to gender the elemental deities, or any of the deities, in the ritual -- keep in mind that Christians and Jews use the SoP, and they've only got one divine gender to work with! If I were doing the SoP in a Shinto concept I'd certainly assign Inari to the north, the direction of earth.