This post may not be canon pending a good night's sleep. I'm le tired.
It was fairly natural that shires would evolve into cities, and then city-states, and then into states proper. The first polity to be recognized as such was probably the jungles around Newman's Dale where the Shamanists dwelt. From almost he beginning of the Bright Way they refused almost all contact with the emigrants south of the jungle. Mostly due to superstitions about the rapidly evolving society and its technology.
Pre-space-age Yih was probably divided into twelve large states and likely numerous smaller de jure independent but de facto client states. I like the number 12 :)
The jungle was effectively a protectorate of the Claravian state immediately to the south, who, after skirmishes with the now technologically outstripped shamanists, forbade all entry into the jungle in the vein of India's prohibition surrounding North Sentinel Island. Alternatively, curious antiquarians venturing into the jungle to investigate the last stone-age yinrih society unwittingly brought novel diseases with them that decimated the jungle population, and their southern neighbor wanted to make sure that didn't happen again.
Regarding the Shakeoff, Neoshamanism was likely most popular in these minor states, who sought to differentiate themselves from their larger Claravian neighbors. The movement romanticizing the old Shamanists coincided with nationalist movements.
Importantly, these minor states where Neoshamanism took hold were far from Newman's Dale. Once Neoshamanism became established, groups of Neoshamanists demanded that the state bordering the jungle grant them entry into the jungle, perhaps because they alleged the state was concealing proof that the Theophany was other than the Bright Way claimed, or perhaps because secular interests in these smaller states knew the Shamanists were no match for a modern military and wanted to claim the jungle for themselves. Most likely it was a bit of both, with the patriarchs of these smaller states using the new religion as a convenient excuse to drum up support for a war of conquest.
Regarding the state bordering the jungle, they saw the saber rattling of these smaller states (likely an alliance thereof) as a threat, and stoked the flames of sectarian tension to expel the pockets of Neoshamanism that were present, forcing them to migrate to the lands ruled by their coreligionists. This in turn caused a migrant crisis (possibly intentional) in these smaller states, which lead to all-out war.
Clergy on both sides were divided between those that saw these political moves for what they were and those that took the bait.