Description:
Skyrim Extended Cut: Saints and Seducers introduces a new worldspace with new quests and NPC's, which means it's theoretically compatible with most mods out of the box. The problem comes, for the most part, from the one single NPC that is edited instead of given a new instance.

Thoron remains the main antagonist, just as he does in the original creation. The result is that anything that edits him and overrides Extended Cut's changes will break the quest, and will do so in a way that cannot easily be fixed. Worse, Extended Cut is flagged as an ESM, so most mods that edit him are almost guarenteed to take priority as they are esp/esl files and will thus load below it.

This mod is the nuclear option as a safeguard against that.I used xEdit to forward all of Extended Cut's changes to not only Thoron himself, but several quest records in order to force the game to load Extended Cut's changes last.

Instructions:
Install the .esp and load it near the bottom of your load order. If a mod edits Thoron/Saints and Seducers in any way, load it below it. Yes, even that mod. Yes, even the item overhaul. Below *Everything*.

Compatibility:
Obviously incompatible with any mods that make the same edits. Again, this needs to be loaded last or you've downloaded this mod for nothing.
This, and Extended Cut itself, are mostly compatible with Artifact overhauls and the like. It makes no edits to the items themselves. It only places them in new locations.

Questions that you might ask:
Q: esl?
A: yes
If the esl version is flagged incorrectly for some reason feel free to let me know.

Q: Will this mod fix Thoron if I've already started my game?

A: It won't fix what's already broken, but will keep him from breaking further.  There's nothing anyone can do about this: Skyrim creates the NPC and Quest records as soon as the save file is created. It's a limitation of the game engine, and trying to modify a save in such a way will make more problems than it will solve. This patch is for those starting a new game, in the hopes that they might not have to suffer as I and others have.
That said, install it anyway. It'll prevent any other mod's changes from interfering further, and will make brute forcing your way through the quest easier. I hope.

Q: If Thoron is already broken, what are my options?

A: The best case scenario is that you muddle through the unfortunately broken quest using a combination of console commands and the wait function.There's a guide in the Articles section detailing what may or may not work for you. Everyone's game is different, so I make no promises, but it should help. maybe.
The worst case scenarios are that you either leave the world space and give up, or start a new save after you've applied my fix. These are the most undesirable options, but may be your only recourse if even console commands fail to save your quest playthrough. If you chose to simply leave the quest behind and keep playing, I recommend using AddItemMenu - NG or a similar mod to give yourself any rewards you might want. 

Good luck out there.