I think his references to Izanagi and Izanami were probably standard to in/yo ho as it had come down from Yoshimitsu Minamoto. Others may not have been standard in/yo ho, but were possibly shared by Sokaku Takeda, who was also deeply influenced by Shinto. Yet other beliefs and practices would have come from Omotokyo. And I don't know enough to delineate the differences...but I think Izanagi and Izanami may have been how all in/yo practitioners thought of it and only Ueshiba gave out so many hints. Also, Horikawa and Sagawa may have given out lots of such hints but not many people heard of them, compared to Ueshiba, who got so much attention. I don't think it was because he was really superior to them (and may not have been better at aiki), but he was a real promoter and he was really a missionary for Omoto Kyo, as well, so he built a kind of missionary art, filled with followers who, like so many missionaries, don't understand what they're selling.
Anyway, I'm guessing Izanagi and Izanami are almost always what he refers to when he mentions "gods" in relation to takemusu aiki.
In the Kojiki they are called Izanagi and Izanami - but in the Nihongi (published just shortly after) they are called the gods of "in" and "yo", which seems fairly explicit to me.
It's also interesting to look at Ueshiba's rewriting of "kami" to "fire" and "water".