Keep in mind that I am no means an expert. This article mostly retraces my own steps in fixing this, and comprises advice from some idiot on the internet. That said, this worked for me.
Firstly: Install the patch and put it last in your load order if you haven't done that already. It won't fully fix Thoron, but it'll prevent further damage and make your job a lot easier. Now, we'll move on to the tools of the trade.

Your Weapons:
I highly recommend you install more informative console: https://www.nexusmods.com/skyrimspecialedition/mods/19250
You'll be using the console a lot. Almost exclusively, in fact. You want it to be as robust and useable as possible. If you've mistakenly cycled away from it giving information on what you have selected, press "tab" until it goes back to the right infobox.
If you see a word enclose in <these> then that's to reference the number/information you need to insert there. The arrows are NOT PART OF THE COMMAND, don't type them into the command console. So if we're using SetStage, you want SetStage Blahblah 69. exclude any arrows or notations from a command.

sqs <questID> : I'm going to be honest and say I forgot what this stands for. See quest stage probably, since that's what we'll be using for. You enter the command, and it returns a number. Used for diagnostics.

SetStage <questID> <number>: The big red button. This brute forces quest stages and twists the game's arm to drive the narrative forward. Has to be used carefully, but this command's going to be your best friend, trust me.

SetGhost 0: When cutscenes happen, the characters involved are sometimes "ghosted" so that nothing can affect them until they've done all their rambling or whatever. SetGhost 0 forces them to no longer be a ghost, so that you can do things to them.

tcl: Toggle collision, also known as noclip. Now you're going places! Literally. Make sure nothing's selected in the console when you type this in, or you'll just noclip the one thing instead of noclipping yourself.

tgm: toggle god mode. I'm workin' here, leave me alone. For when pesky NPC's try to kill you when you're fixing things.

Kill: I shouldn't need to explain this

Disable: The crueler version of Kill. Existn't

The Quests, and how to beat them into shape:

A foreword: If you see Thoron anywhere he shouldn't be, like outside on a path, press your Wait hotkey and wait an hour or so. He's trying his hardest, give him a minute (or more)

The Isle of Madness: You're set on a course to rescue an ally on need. When you arrive there, you'll find that instead of saying words, an unhinged Thoron will be attempting to melt Dylora with spells. This...isn't supposed to happen.
This one's a fairly easy fix for most people.
Step one: Select Thoron using the console. just click where he is, and double check to make sure you've actually selected him. If you haven't, use the mouse wheel to change your selection until he's selected.
If THAT does not work, use tgm to make yourself immortal, then use tcl to move past the barrier and into his personal bubble and select him. If you're still having trouble, just click the barrier and use disable to get rid of it, it really isn't that important.
Now, type the kill command once Thoron is selected. He should enter bleedout, and when he comes out of it he'll warp away and the barrier will disappear. From here, free Dylora and the quest will progress. Finally!
If this failed to work, then we're entering sqs territory. Type sqs EC_SS_MQ101 . This will return a bunch of numbers, with either a 0 or a 1 next to them. So for example:
Stage 31: 1
Stage 32: 1
Stage 33: 0
etc, for example.
Your lucky numbers for this quest are: 31, 35, 38, 39, 40
These are the main hallmarks provided in xEdit.
Check which numbers the command gave you. Then move sequentially forward from the first number to be marked with "0" using SetStage EC_SS_MQ101 <insert number here> (but without the arrows). So if you used sqs and got 33 as the first 0, as in my example, and the quest is still stuck, type in SetStage EC_SS_MQ101 33, THEN progress to the next number if it's still not working.
With that, we're moving on Thoron shouldn't appear until the last quest in the mod, at this point. However, there's the real possibility that he may end up on the main road outside. If you see him out in the world, use the Wait option and wait an hour or two and he'll make his way to where he's going after he catches his breath or counts rocks or whatever he was doing instead of being where he needed to be.

The Roots of Madness: Take a deep breath, and obtain a serving of your vice of choice (wine, a joint, etc), because this is going to be stressful. This quest gets screwed hard by any mod conflicts, and we're in too deep to fix it with simple load order changes. After all, if that were an option you wouldn't be putting up with me.
For sqs, the command for this quest is sqs EC_SS_MQ102.
Go down to the final dungeon, break the funny wall, and confront Thoron. If you installed my patch, he should function properly for this part. He did for me, anyway. He'll yammer a bit, then he and his goons will turn hostile. Progress normally, and kill them all. Thoron should, at this point, shout some nonsense and break the floor. If he doesn't do this, it's time for the sqs and SetStage commands again!
I have no clue what the numbers are for this, since I didn't need to use these commands here. My advice is to use sqs and then use Setstage to set the stage up in increments of 1.
You'll be prompted to jump down into the hole. Once you've done so, Thoron summons two copies of Staada and Dylora to attack you. If they do, great! But they probably won't. They'll run at the walls or stand in place. They've inherited Thoron's madness. Oh no!
Type sqs and take note of the 0's and 1's. It should indicated that Stage 79 is 1 and Stage 80 is 0, meaning you've completed 79 and haven't completed 80. Okay, great!
If you really, really want to, you can select Staada and Dylora and type startcombat player. This let you fight them if you feel cheated out of a fight. Otherwise, just select them and type kill.
type sqs EC_SS_MQ102 again. For me, this returned Stage 79: 1 Stage 80: 0 Stage 85: 1 . Ooooooookay?
This probably means something to a more intelligent mind, but you got me instead. If Thoron hasn't come out from behind the barrier, Type SetStage EC_SS_MQ102 86 .This will dispel the barrier and bring Thoron down to your level to fight you. He'll already be in combat when you do this, so be aware that he'll come out throwing hands (or spells, or sword maybe).
Fight him normally, or kill command him. It really doesn't matter. If he is invulnerable at any stage of this sequence, use setghost 0 on him and he'll be forced back to the "real" world with the rest of the proles and allow you to beat him stupid(er).
After losing, he'll enter bleedout.  Wait for him to stand again. He will STILL be in combat while the next cutscene starts; I recommend using tgm to go into God Mode at this point, since you can't kill him but he can still kill you. That's cheating, so cheat back.
If he gives his dialogue about asking his Lord for help normally, and you're teleported up you're done! You don't have to do anything else. If that DOESN'T happen and the white screen stays, we've got to enter another command. If you care, sqs should return Stage 88: 1 if this happens (meaning Stage 88 is complete), but will also return Stage 89: 0.
But you only really need the next one. SetStage EC_SS_MQ102 89 should finish things up. This wins the fight and teleports you back up, sans white screen. Congratulations! You won the mission!

Now, one more mystery presents itself. Where's Thoron's body? There isn't a body. This isn't a bug near as I can tell, either. He's become the funny crystal at the back of the room. Brutal.
But this doesn't help you if you wanted something off his corpse. The main offender is the Sword of Jyggalag, but there might be other things mods added in you might want. Either add them in using the console, or download AddItemMenu and use that. If there's another way to obtain the sword, I haven't discovered it, and judging by the comments on the main page nobody else has either.

Either way, good job! You overcame monstrous odds in service of a goal that should have otherwise been a cakewalk.