Some story questions after the final boss *spoilers*

[P4wn4g3]

I'm confused on a few points after beating the final boss (the first time) and getting through the story. Idk how many of these things are expanded upon in NG+ so I'm not asking for spoilers on NG+ stuff, just clarity on what I'm supposed to know to this point.

Lamech's secret chamber - I don't get the significance of this place, maybe it's explained later.
J - I assume is Jonah.
Z - No idea who this is, was I supposed to know? The only Z ever mentioned that I'm aware of is Zoe, one of the gongheads.
The Rebellion - Some uprising against the Estuaries, Enoch mentions in a memory that I should understand the rebellion now but I don't. Don't know why it happened, I assume it was to overthrow the Estuaries but that doesn't make too much sense. I don't see how this ties into any one Estuary's plan or the King's plan, other than to cause death and empower them with more souls. So idk maybe Jonah instigated it to become more powerful, but the other Estuaries don't seem to have any awareness of the rebellion, though it's implied the King does.
Stygian Beasts - Are these things supposed to be an Estuary? Cuz they appear on the door but they are just giant zombies.
Monsters and black roots - It's explained all the monsters are a product of the root fungus that is spreading for unknown reasons. Somehow the rebellion war introduced this, I'm pretty unclear as to how. The flooding in the deep mines was caused by the Styx overflowing.
Naamah stuff - Why did Naamah want to trap the dragon? Seems like that goes against her code and ended up being a dumb idea, also they could have freed it and the blights it caused would have gone away.
Irad - All he says seems to add up to him getting poisoned and betrayed by Enoch or I guess Jonah, but I don't know what his plan was ever supposed to be. I guess he is trying to govern, which seems like something all the Estuaries do. Not sure if they are blaming him for all the problems happening or what. Was he trying to kill the other Estuaries to make the fruit of life? Seems like ultimately Jonah rang the Bell of Return and caused the Ceremony of Return to start, which Lamech wanted. And Jonah poisoned Irad. I guess Philosopher Nous is actually Enoch or directly controlled by him.
Enoch's memory - I don't understand much of this, I guess he's directing Jonah to do some stuff. Understanding the nature of the rebellion, the bell of return being the only path of escape, and later at Eden the vial is on the shore so this was definitely directed at Jonah, but I'm not connecting all the dots here.
Subterranean Kingdom - This doesn't make any sense to me, Tubal says that Enoch has mimics above, i.e. in the Stygian Library. He mentions Estuary Jabal (is this supposed to be Jonah?) and Estuary Adah (Quinn maybe? idk) and other Estuaries. Idk who these are. The Estuaries Lamech - Tubal all know each other and are self described siblings. Jonah and Quinn being outliers. Is this place supposed to refer to the place you pull the castle to at the end of the game?
Tubal's rebellion plan - ok so tubal long ago planned the rebellion, but he describes it as a rebellion against the king and a fight with the overland Estuaries, whoever they are. I'm not sure how that links to the rebellion the other Estuaries mention and Jonah is leading. Either way, Tubal betrays the King to grow new fruit and become god king. Idk how that's different than Irad's plan other than giving the fruit to the king. And it seems like the king was aware of this plan and wanted it to happen for the fruit to grow anyway. If the goal here was to overthrow the above world Estuaries, why would Jonah have agreed and have taken part in the plan? I guess because he is the estuary of betrayal? Kinda doesn't make sense seeing how he'd be an intended target. Or is Tubal's plan one that is thwarted and completely unrelated to the rebellion that happens later?
Tubal's location - I don't get who could have figured out what Tubal was doing or who had the power to sacrifice him to the dragon. They must have also poisoned him though, and by doing so poisoned the dragon.

[Gnodab]

I'd recommend just playing through to NG+7, it will explain most if not all of your questions. Notably, by enabling Burdens for NG+ you can fight stronger versions of each boss, and after each fight there is a huge lore dump for that boss that ties into the greater narrative. More Scars also become available that add more insight.

I would answer your questions, but it's way more fun to discover the answers in-game. If you're still confused afterward though, feel free to ask away.

[Monsieur Muh]

Agree with @Gnodab, the lore of the game is really, really great, even if most people won't be interested enough to try to have a full overview.