Is there supposed to be a version of the Eight Divines in every pantheon? It doesn't seem like there is. The Eight seem to have clear correlations throughout all the human pantheons, but not in the elven ones.

I've seen Y'ffre called an aspect of Kyne and that Kynareth is a combination of the two, but then why do both appear in the Khajiit pantheon seperately?

I think all deities ultimately relate back to the eight Earthbones, but that doesn't mean they have to be a one-to-one thing. The only two Gods who are guaranteed to be present in every pantheon in some way or another (at least insofar as we know, and I think there are some that lack even them) are the Time Dragon and Space God, Aka and Lorkhan. Other than that, bets are off, I believe.