Just not sure it’s worth it, I suspect this is going to require way more tech knowledge to dig in to than I possess!
It really shouldn't. It's designed to be a nearly hands-off process with instructions on the few fiddly bits. In fairness, I installed Living Skyrim 2 with no issues, but haven't had time to try the updated version. I'll give it a shot this weekend and see if I run into similar issues.
I find the MO2 program a little confusing. After Living Skyrim was downloaded I had multiple files flagged as needing authorization by the author or something like that. Unclear to me what is required to resolve that.
Depending on the exact message, it sounds like it might be trying to tell you to connect your Nexus Account to MO2. In the MO2 options theres a place you can put your Nexus credentials in so it'll log in for you. Its necessary for updating mods via MO2 and for having MO2 handle downloads from Nexus, but Wabbajack should have downloaded everything already so that shouldn't be an issue. You did put your Nexus info into Wabbajack before letting it download, right?
Another thing to check is that you're launching it through skse_launcher.exe and not launching the game through Steam or Skyrim's normal launcher. Lots of the mods won't work if you don't launch through the script extender.
I had Nexus connected and did launch through skse launcher.
Maybe I’ll have to try it again and screenshot the weird stuff I’m seeing to get a consult from you fine folks.
Basically ignore anything that isn't automatically provided by the Wabbajack installer, or noted in the Living Skyrim 3 readme/install guide. I haven't touched anything in the supplied MO, other than to enable the Quickloot mod and the UI texture for it, as noted as optional steps in the readme.
The trick is to *not* think about what you are doing. Dont second guess or try to 'fix' anything, just do exactly. what. the. guide. says. and ignore what you see on screen 
Dont add or change anything with the supplied MO instance. Updating of mods etc should be done via Wabbajack, and not inside MO.
The game should be launched from inside MO using the big 'Play' button in the top right (there's a button underneath that can be used to create a launch shortcut on the desktop so you dont have to actually load MO first manually).
I'm happy to sit on a call in Discord with you (or anyone else for that matter) to get this up and running, if that would help.
Really is quite something...
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