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Nexus Mod Manager is not all that complicated, but it can seem a bit overwhelming without a good, step by step guide. I'm not sure if there's an up to date one, and I know the NMM has changed a lot recently, but Gopher's YouTube guides are still a decent overview of the general idea of it. https://www.youtube.com/watch?v=ClqtmSUsFhg
LOOT is a very straightforward tool, all you really need to do is hit the list icon to sort and then hit apply when it's finished, assuming there's nothing dreadfully wrong (like missing master files) it shouldn't take more than that. Here is a video by GamerPoets: https://www.youtube.com/watch?v=zOocsSaj0fs I believe he's going to be making a guide to the newer versions of NMM, although like many serious modders he prefers Mod Organiser, I believe.
Personally, I don't use AFT on 'serious' playthroughs (i.e. ones I intend to last more than a couple of dozen hours, and I'd be upset if they got broken) as I've had issues with it bugging out on me before. It's not compatible with mods like Interesting NPCs, either, and some individual follower mods don't like it. My follower manager of choice is Extensible Follower Framework (which actually has a *functioning* patch for Interesting NPCs).
Speaking of individual follower mods, are you using the Workshop version of Inigo or the vastly improved v2.2 from the Nexus? I would STRONGLY recommend you get the new one - this will require a new game, but so would switching from AFT to EFF.
The Steam Workshop works perfectly fine for games where mods are 'plug and play' but it's honestly not fit for purpose for Skyrim, because you can so easily wreck your saves by uninstalling or even sometimes updating mods mid-game.
There are a few outdated and/or superseded and/or conflicting mods in your list I think, and your sort looks to be off in at least a couple of places. The thing is, once you have more than a couple of dozen mods, the WS becomes a very poor way to manage things.
Not pushing you to move to Nexus, but I think I would whittle it down to a dozen or so "must haves" and leave it at that and then hand sort them based on knowledge gleaned here or in the read me files.