Oof. Let's see here:
Control members: Liz, Tiana, the Ghoul (I think I called him Jake), Deus (robot), and some guy with a blind-fold on who I never did much backstory for. As for the number of Tiana's, I never put a firm number on that.
Conspiracies are controlled by their wish to remain hidden: not sure where I got this one. Probably something Ken Hite
wrote helped inspire me.
Gatekeeper to Heaven's Door. Wasn't meant to be an official title; mainly there to set up the Ghostbuster's reference in the next panel. ("I am the Gatekeeper! Are you the Key Master?")
Gladius Dei arriving while Sirrus' attempt at Deicide: I kinda hand-waved this one. Assume that the forces of the Angelic Host let them know, but were unable to intervene themselves due them having to keep all of reality held together in the interim.
One/Many/One and the Cycles of Sirrus: as Guildenstern guessed. The first was a reference to Yggsdrassil, the second showing that Sirrus has always been a pawn. Even in his moment of greatest triumph, he was being used by Kali.
Jack and Thera during the reality warp: I never really thought this out. Truthfully, I'd write it differently now. Drop the anime thing, go with something more surreal. Maybe a Grant Morrison type of thing.
Hope that alleviates some of your confusion!