Kannazuki no Miko/WMG

Chikane and Himeko are "book reincarnations" of Eve and Hazuki from Yami to Boushi to Hon no Tabibito.
Eve is not above writing multiple versions of a character (Hazuki herself exists in two books, albeit they are tracking copies of one another). She has been known to mess with peoples' "destinies" as well (Gargantua, Ritsuko, etc). The characters in question are very, very similar-looking, especially Chikane and Hazuki, and they share personality traits, too.

Chikane and Himeko were reborn as Kaon and Himiko in Kyoshiro to Towa no Sora
And that one scene after the credits actually takes place in the alternate universe of Kyoshiro rather than in the Kannamiko world.
 * This troper is of the opinion that this is accepted fact within the KNM fanbase. What he's trying to say is that if Kaishaku is going to make a series about reincarnating lesbians, and then have two characters who are definitely those girls take place in a series with a similiar aesthetic and which takes place far enough in the future for them to have lived and died then it would make sense for them to have been reincarnated for that particular misadventure.
 * It is this other tropers understanding (i.e. Wikipedia says so) that Kaishaku has made several manga the involve Chikane and Himeko (as well as Souma) to some extent and that most simply haven't been made into anime.

There is another shrine... on the Sun
OK, so we have two priestesses, one associated with the sun, the other, with the moon. This symbolism is evoked all the time, so there's probably some metaphysics to it. In the end of the series, the priestess of the moon is imprisoned in the shrine located on the moon. Keeping the sun-moon motif, we must then assume that there is another shrine on the sun, reserved exclusively for the Solar Miko. Please think of the catgirls before you ask me how...
 * That one might actually be well built, given that the lunar shrine apparently can't support 1/6th it's own weight (taking the moon's gravity into account) whilst still in pristine condition (it had better better be, given that it's on the moon of all places) I would have to assume that it is very terribly built.

Himeko is tainted by Chaos (yes, the Warhammer/40k Chaos)
Brown is the original eye colour, with blue and green being seemingly benign mutations of the original gene. Himeko's eyes, however, are purple, which leads this troper to conclude that more than mere genetics is at play, and that the foul energies of the warp exist within Himeko. Given that the Warp seems just as fond of purple as it is of red, one can expect that anything Chaos got it's hands on but didn't want announced would still retain a subtle branding of sorts, and a discolouration of the eyes is about as subtle as it gets, it's insidious, as is the ways of Chaos. As for why the taint is present, perhaps it gives Khorne a little bit of the action during the sacrifice. Or maybe, since the Orochi are as hostile to them as to anyone else, it makes the sacrifice work a little better. Either way, try keeping that in mind next time you (the reader) watches the Kanna Miko.

The Orochi is really an Anti-Spiral Spiral annihilation system...
...and the whole 'priestesses summoning a God to seal it away' thing is just people accessing spiral power without knowing what it really is.

Himeko and Chikane are reincarnated as Yuki Nagato and Mikuru Asahina at some point.
Actor Allusion aside, there is a very similar relationship between Yuki and Mikuru to the one between Himeko and Chikane (At least, if you look closely enough). Also, for some reason I just love the Irony that comes with the idea of Himeko becoming a big chested girl everybody lusts after, while Chikane becomes unpopular girl who is hardly noticed.

Chikane is a Mark II Steel Angel.
Consider Chikane's dual roles as the Lunar Priestess and one of the Orochi. Next, consider that despite being created to protect humanity from Demonic Invaders the Mark II Steel Angels are all half demons themselves. Finally consider Kaon whom many believe to be Chikane reborn. Kaon is an Absolute Angel which are the successors to the Steel Angels.