Okay, this is all very entertaining to read through and I have a few thoughts:
1. Shar and Selune have been featured prominently throughout. Where do they fit in?
2. Moonrise Towers. The one main difference between the True Souls and our merry band is that our guys have never been to Moonrise where the post-tadpole indoctrination supposedly takes place. The TSs think they are serving a goddess and are blissfully unaware of the pollywogs in their heads.
3. Are Mizora and the Grand Duke being held for a particular, perhaps additional purpose? They were certainly chosen for insta-transport to Moonrise.
I think there are at least two factions vying for ultimate control, with other stickling their fingers in wherever they can*, or just trying to get a piece of any potential pie.**
*Who is it that was "right as always" and sent our skeletal friend to bring back our fallen? Did they (or someone they are allied with) alert the kithrak to the ship's location in the first place?
**Raphael, and who knows who else.
