Does Mora really have your soul at the end or is he just expecting you to stay in his realm or to keep coming back because you are dragonborn and have the same lust for power that Miraak had? If you were to just never go back to his realm after the final quest in Dragonborn would he even have any power over you? He can't just drag you back there while you are in Nirn as it's been shown he can only manifest physically on Nirn from the Black Books.

Why didn't Mora just kill Miraak if he knew Miraak was conspiring against him instead of waiting for you to nearly finish him off? Why did you even need to nearly finish him off anyway? What did Mora actually gain out of all this in the end?

When you read a Black Book other people say they can still see you but you are transparent as if you aren't really there and if you die within Apocypha, you are sent back to Nirn. I assume this is different for the last quest in Dragonborn because Miraak will absorb your soul if you die. What is actually going on when you read a Black Book, anyway? Does the same thing that happens to you happen to other people?

Miraak got to Apocypha through the Black Books too, didn't he? So why if you go through the Book does part of you stay on Nirn and you get sent back when you die but Miraak ends up a skeleton meaning his entire body was in Apocrypha? Why do people say they can see you transparent which must mean some part of you is left on Nirn when you read a Black Book instead of you being pulled completely to Apocypha like Miraak?

I realise you can't because of them being marked as quest items in the game, but what would Mora do if you were to get rid of the Black Books instead of returning to Apocrypha ever again? Would he be angry with you?

What are the extent of Mora's abilities? Does he hold the ability to actually influence fate or is he just able to very acurately predict the outcomes of things and know how to bend things in his favor because of this? Is he sort of like an Elder Scroll? He must have some limitations if he needed you to fetch the secrets of the Skaal, and being a Daedra he can't just meddle with Nirn as he pleases.

-Because just killing Miraak means he would have no replacement servant, nor would he have been able to use you to get the secrets of the Skaal.
-Mora wanted to see if you were truly stronger then Miraak, and thus worthy to be Miraak's replacements as Mora's servant.
-You, to replace Miraak, as his servant, and the secrets of the Skaal.

-Well, it's entierly possible your soul is sent to Apocypha any time you read a black book, you being sent back if you "die" is because there is nothing around to absorb your soul.
-Depends, people who are just reading the books do, but some can be dragged into Apocypha fully by Herma Mora, if they get to lost in all the forbidden knowlege.
-At least some point in the past yes.
-Becuase Miraak was a servant of Hermaus Mora, he sold himself to the Daedra, and thus the Daedra has more power over him, including the ability to fully bring him into his realm.
-Becuase Herma-Mora doesn't decide to trap you in Apocypha, you are usefull to him in the outside world.

-The black books are a part of Herma-Mora, and his realm, if the Dovahkiin just left them somewhere, Herma-Mora would just have them dissolve back into his realm, and he would then place them in the world again. It's the same as ow Azura's star fades back into her realm every hudnred years or so, as mentioned in her quest in Skyrim.
-Not really, you already tasted his forbidden knowelge, using it ever spreads his influence, and his black books being gone for a hudnred years is like a day to an immortal Daedric prince.

-Unknown
-Probably just really really good at being able to predict things.
-No, Elder Scrolls are fragments of creation that know everything, except what happens in Dragon Breaks, Herma-Mora, while knowing a lot, doesn't have the power of an ES IMO.
-You are correct on him having limits.