Hello BronzeAger! I'm glad it's helpful. To answer your questions:
1. "When you write that shamanic faiths are receive Empyrean or Chthonic influences, do you mean that the Spirits which Shamans engage with tend to fall into either the Empyrean or Chthonic camp (as primitve or perhaps ancestral aspects of the syncretic deities) or do they occupy a middle ground, or are they something else entirely and not really comparable?"
An Empyrean cleric would say that the Empyrean gods are true gods, worthy of worship, while the Chthonic gods are demons, whose worship is evil. Empyrean clerics also permit prayer to ancestors, heroes, and emporers, revered as "exalted", in a manner similar to how saints are prayed to.
A Chthonic cleric would say that Chthonic gods are strong powers worthy of worship, while the Empyrean gods are weak powers unworthy of worship. Chthonic clerics would also permit prayer to undead sorcerer-kings and various lesser demons and idols that serve the Chthonic gods.
A Shaman would say that the Empyrean gods are strong spirits that hold sway over civilization and some gentler aspects of nature, the Chthonic gods are strong spirits that hold sway over dangerous forces of nature, and that there are many other powers too, ranging from exalted ancestors to nature spirits to forgotten powers. They would say that some or all might be worth worshipping at some time or another. Perhaps Dirgion, Chthonic god of death, is given an offering to avoid his evil eye, while Ammonar, god of sun, is asked to bring warmth on winter nights, while the local river spirits are placated during flood-season.
Think of an Empyrean-influenced Shaman as one who worships Empyrean gods alongside various other powers in a traditional folk religious sense with mythology but without theology. A Chthonic-influend Shaman would worship Chthonic gods alongside various other powers in a traditional folk religion with mythology but without theology.
2. "I ask because in a lot of recent implied settings the spirit world of the druids tends to be cast in an 'Old Faith' way - they essentially become Chthonic, but not necessarily Chaotic - while th gods of the clerics seem to be the 'New Gods.'"
In terms of age, the oldest religions are the Farahavar-Empyrean faith and the Khepri-Chthonic faith. These largely disappear during the Cataclysm of the Day Without Night. The survivors (various men, elves, dwarves) are left with a Shamanic folk religious faith that echoes the forgotten religions.
The Khepri-Chthonic faith enjoys a renaissance circa 2500 BE when the elves learn the Chthonic faith from the Great Teacher (a surviving khepri) in Southern Argolle.
The Farahavar-Empyrean faith returns circa 700 BE when the prophet Azendor revives their worship after receiving holy books from Mt. Audarammas.
So from the perspective of the present-day inhabitants of the setting, the Chthonic faith is older, although in fact both are quite ancient.
3. "Also, have you written about Farahavar and Khepri (a proto-Egypt?) before? My instant reaction when seeing your reference was to think of legendary ancient supercivilizations like Atlantis or Lemuria but I may well be way off on that."
You are 100% correct. The Farahavar are Lawful arcane/divine casters, while the Khepri are Chaotic psionicists. Both have advanced "scientific sorcerery" no longer available in the current setting.
Their existence is hinted at occasionally in ACKS and various other writings. They are the races that ruled the land before the Day Without Night. They are now more detailed in Lairs & Encounters. [NOTE: In the *original* homebrew Auran Empire setting, the Khepri were the Mind Flayers and the Farahavar were Solars. I needed replacement creatures for professional publication. One of the high-level backer rewards available in L&E was the opportunity to create new monsters, and Mark Bober and Charles Myers were kind enough to back at that level and bring these two races into existence.]