Telsler

Before you go with the nuclear option, try checking your other f4se plugins. For example, transfer_settlements.dll causes my game to ctd at main menu even though it doesn't show an error, because that mod hasn't been updated yet. Edit: You have to actually move/delete the .dlls in order to stop them from loading.

The only reference I can find to hud extension is Nameplates - Floating Healthbars by expired6978. http://www.nexusmods.com/fallout4/mods/21636 If you have this, there's an update for the latest f4se.

You need to update LooksMenu. The error is telling you that LooksMenu is checking for an older version of the game.

Terminal+ is Transfer Settlements. Need to wait for the plugin to be updated.

03 SMIM Lantern. Optional install of Enhanced Lights and FX (ELFX) changes the texture of that lantern to a custom location, but does not include the texture. either delete "Meshes/clutter/common/candlelanternwithcandle01.nif" OR install SMIM.

Yep. Wrye Bash doesn't care where the mods come from as long as they're in the data folder. you can install them manually, with NMM, MO (launch bash from inside MO), or any other program.

Try "setstage VC01 0". this should in theory set the quest to 'not started', rather than 'completed'. I can't test it myself, but it should be obvious right away whether it works or not.

Only explanation I can offer is that you had mods. I can certainly understand you wanting to get a second opinion though. You can always try verifying your files through steam, too.

Invisibility is usually caused by missing meshes. check for "meshes/actors/SkyBrutal". If it's missing, you need to install one of the two mesh packs from deadly mutilation's mod page. this is not installed with the "CORE" pack.

There are no other folders in vanilla. all that data (aside from the ones you mentioned) is stored in the .BSA files. This is normal.