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If you did not remove all of the mod's scripts, or if it replaced a vanilla script that was not restored, then that can cause it.
The one thing all of those locations has in common is a fire pit, so you may want to look at the Embers mod, or any mod that affects interior cells, like More Idle Markers if it gives NPCs more markers in interior cells as the name suggests.
It may not be a mod conflict so much as it is the game having trouble processing something in an interior cell related to such a mod - shadow lights, adding NPCs, searching for dialog files for them, atmospheric effects, etc.
Also see if your timescale is too low.
Disable auto saves.
Use LOOT to sort your load order if you are not already. Cut down on heavily scripted mods. Clean your master files. Verify your game cache using this checklist by Ilja:
One or more of your master files (Skyrim.esm, Update.esm ect.) is damaged, or otherwise messed up. It needs to be fixed.
Exit Steam.
Go to Steam folder and remove folder named appcache
Close your computer and let it cool off a little, to clean your registry cache. Take a peek outside the window to see how the weather is.
Start your computer.
Start Steam. Let it load for a while, when it is inspecting your game files for new appcache folder.
From Steam client Library view, right click the game with your mouse.
Select Properties > Local Files > Verify Integrity of Game Cache...
* 1 file will always fail to validate. It is related to how Steam detects your graphic card configurations and has no effect to your game.
* If you had cleaned your master files with TES5Edit, you will have to repeat the process. Steam will consider them modified and replace them.
There are problems with Immersive Patrols. I'd lose it. Also, while it's said that you can use Immersive Citizens and RDO together, I would not recommend it. The load order is tricky. Pick one or the other.
Immersive Armor adds a great deal of stuff to the game. Pick a couple of good armor mods and be happy. You don't need to add all that stuff to the NPC's.
The JK mods are really hard on the game as well.
Do NOT remove mods mid-game. If you're going to remove some, start over.
EDIT: I would also be concerned about Open Cities. Almost every mod I look at has an Open Cities patch. When a mod needs that many patches, I don't use it.
I can't speak for the rest of the instructions you offered, but Open Cities requires patches for other mods to work because of how it works, not because the mod author left a lot of things to be fixed. It doesn't just move the cells for the cities into the overworld. It recreates the city inside the overworld and disables access to the city's interior cell.
If you play with Open Cities and use a mod that adds a location inside one of the cities, a patch is necessary so it alters the correct cell, and exit out into the proper city. If you don't have a patch, you end up in a mostly abandoned city with no doors actually working to take you into other cells.
Just want to point out that I've ran numerous stable modded BethSoft games (TES3-5, FO3-NV) and I've never cleaned my masters and stopped needing to clean anything past Morrowind's mods since I only use well-updated, tested and endorsed mods. Read descriptions carefully and learn to predict incompatibility purely based on what a mod DOES. And always have the unofficial patch which exists for all the mentioned games.
There's much better advice to give than the 5 people here parroting "clean your masters."
Topic:
The Doc is right that if he removed the mod but didn't close the game or started a "new game" from a save (like right outside of Helgen) then Game #4 would probably still have problems.
What he did not mention is that "updating mods to their newest forms" is another way to accidentally screw up a current save. Most descriptions will tell you a detailed process needed for updating the mod mid-playthrough and recommend a new save instead.
TL;DR
Pretty much everything you've done to "fix" this has resulted in needing a brand new clean save. Start there and get back to us.