I use Mod Organizer 2 as it doesn't touch the game with NMS caused me so many headaches over the years, Normally with these you have to reinstall the mod to change the settings heres my list if it helps anyone atm.
Also guide here for anyone doing
Fallout 4 mods
+Weapon Debris Crash Fix
+Merchants Sells Weapon Mods
+Larger Shipments - Gold Fix
+Larger shipments - better prices - more shipments - vendors sell all
+Sim Settlements 2 - The Bleachers A Diamond City Story - Patch
+Dogmeat - A True Companion
+Companion Whistle
+Jetfuel Radio Standalone
+OLD WORLD RADIO - BOSTON v6.0
+More Where That Came From - Diamond City Radio Edition
+LOST AWKCR VIS-G Patches
+Simple Salvageable Power Armor Frames (SSPA)
+Excavator Power Armor
+Midwest Power Armor Evolution
+Submersible Power Armor Redux - BioShock Inspired
+Raider Power Armor Chop-Shop
+Standalone Construction Power Armor
+T51c AirForce Power Armor
+Liberty Power Armor
+Eff's Weaponsmith Extended Integration Patch - Ak5c
+Ak5C - A Nordic Relic
+Weather Synergy - Merge Patch
+True Storms Wasteland Edition v1.4
+Atomic World
+Stumble Upon Interiors
+Keep Radiants in the Commonwealth
+The Bleachers - A Diamond City Story E-Tex
+The Bleachers - A Diamond City Story AE Patch
+The Bleachers - A Diamond City Story
+Lima Detachment
+Fallout 4 Northern Springs DLC LOD
+Depravity - VIS-G Patch
+Tales from the Commonwealth AE and VIS Patches
+Tales from the Commonwealth Visual Fixes
+Outcasts and Remnants - Loads-ASE-WSE2-VIS Patch
+Graf's Security Fences
+No more gaps under junk fences
+Homemaker - Expanded Settlements
+Gun Fixes 2
+Better The Third Rail Patch
+Better The Third Rail
+Less Loot D.E.C.A.Y
+Vault Looter
+FO4 Bug Fixes Pack (by Sakura9)
+Unique Settlement Vendors - Protected and Tracked
+Rusty Face Fix
+Water LOD Fix
+Real Water HD
+Delightful Dead Fish - HD Retextures for the Commonwealth and Far Harbor DLC
+More Spawns Scripted Version (with in game menu)
+Scrap Everything
+Build Limit Remover
+Shipment Biggest
+Nuka-World Bottle Scenery Fix
+Cubemap
+Scrap-O-Tron 2000
+True Grass
+NPCs Travel
+Legendary Clothing Loot
+Legendary Helmets
+Legendary Power Armor
+Less Crap Debris Textures
+Fixed Gobo Effects
+Open Season Enhanced
+Croup Manor Navmesh and Pathfinding Fix
+No more floating razorgrain
+More Bobbleheads
+New Magazines (FROST)
+Lucky Loot
+Lootable Cars And Trucks v2.0 all DLC. (EN) and (RU)
+Lootable Cars
+Vivid Weathers
+FogOut
+English Strings for Fallout 4
+Craftable Turret Stands
+Extended weapon mods
+Combat Rifle Mod Restoration
+Fixed Alpha Maps
+Wall Pass-Through Power Conduits
+4K Gnomestraviganza
+Lootable Vault Suit Boxes
+Uncapped Settlement Surplus
+Glazing - Windows With Glass (WWE)
+General Dave's Wasteland Walls
+Floors - Roofs - Walls
+SavrenX HD DLC Armor and Clothes
+SavrenX HD Vanilla Clothes Fix
+SavrenX HD Vanilla Clothes
+SavrenX HD Vanilla Armor Fix
+SavrenX HD Vanilla Armor
+SavrenX Food and Foodware
+SavrenX Organic Gore
+SavrenX Creature Pack DLC REDONE
+SavrenX Better Robots and HD Liberty Prime
+Weapon Smith Combined
+Vendor Caps
+See-Through-Scopes
+New Calibers
+Loads of Ammo - Switchable Ammunition Types
+All Settlements Extended
+Workshop Menu Missing Tabs Fix
+Longer Power Lines
+D.E.C.A.Y - Better Ghouls Patch
+D.E.C.A.Y - Better Ghouls
+Plutonium Creatures
+Wasteland Imports - Goodies from all across the Wasteland
+Better Cooking Stations Patch
+Better Cooking Stations
+Diamond City Expansion
+The Machine And Her
+Xander's Aid - DLC
+50 Ways to Die at Dr. Nick's - Quest Mod
+Welcome to Goodneighbor
+Depravity - A Harmless Bit of Fun
+Ransacked Relays and Shuddersome Subways
+Nvidia's Vault 1080 Patched and Optimized
+Atomic Radio and Tales from the Commonwealth TC
+Atomic Radio and Tales from the Commonwealth
+Outcasts and Remnants - Quest Mod Plus
+Fusion City Rising - Quest Mod Plus
+Beyond the Borders - Far Harbor fix for version 4
+Beyond the Borders - New Lands Mod World Data
+Beyond the Borders - New Lands Mod
+Fallout 4 Northern Springs DLC
+South of The Sea. (Massive GS and more Expansion) (Final Update July 2020) Patch
+South of The Sea. (Massive GS and more Expansion) (Final Update July 2020)
+Glowing Sea EXPANDED (More Loot Buildings and Enemies)
+Combat Zone Restored
+Better Skylanes Flight 1665 (Glowing Sea)
+Sim Settlements 2 - Pra's Random Addon 2
+Wasteland Venturers Sim Settlements 2 Addon Pack
+SS2 Superstructures - A Sim Settlements 2 Addon Pack
+Sim Settlements 2 - Ruined Homes and Gardens 2.0
+Sim Settlements 2 F
+Settlement Menu Manager
+Place Everywhere
+Stay Focused Son
+The new settlers a plus Overhaul vanilla
+Immersive Mouth and Teeth - 6.0
+Nasty Nisha
+Money Mags
+Mighty Maxson
+Mesmerizing Magnolia
+Manly Mason
+Kind Kasumi
+Determined Desdemona
+Charming Cito
+Captivating Companions
+Merged Fixes Visuals
+deLuxe Makeup Mask
+deLuxe Makeup
+Ghastly - Ghoul Eyes Texture
+The Eyes of Beauty Fallout Kaleidoscope Edition - All-in-One
+Commonwealth Cuts - KS Hairdos - ApachiiSkyHair
+Misc Hairstyle
+All Weapons HD (A.W.H.D.)
+CROSS_Chosen_Of_Atom
+VIS-G Item Sorting Synth
+Synth Overhaul - By Maaro and Echoes Patch
+Synth Overhaul - By Maaro and Echoes
+IEX Suit AE VIS patch ae
+IEX Suit AE VIS patch
+CROSS_InstituteExpeditionarySuit CBB
+CROSS_InstituteExpeditionarySuit
+Super Mutant Redux 2.0
+CROSS_BrotherhoodRecon
+Improved BoS
+Armorsmith Extended Raider Patch
+Raider Overhaul WIP
+We Are The Minutemen
+PreWar Binoculars
+Tactical Flashlights
+K-9 Harness -- Tactical Body Armor and Backpack for Dogmeat
+Mercenary Outfit Mash-ups
+The Mercenary - Pack
+Holsters and sheaths
+Just Visible Holstered Weapons
+Visible Weapons - 3rd Person Holster
+QuickTrade Redux
+Ultimate Colored Vault Boy Animations Overhaul
+Alex's Male First Person Camera Height Fix
+Crafting Framework - Ammo . Armor . Junk . Legendary . Weapon
+TRUBY9 ULTRAWIDESCREEN DEF_INV compatibility fix
+TruBy9 UltraWide Fallout 4
+VIS-G Item Sorting
+Immersive HUD - iHUD
+Power Armor HoloHUD
+HUDFramework
+DEF_UI 1
+DEF_UI
+Extended Dialogue Interface
+CBBE Underwear Retexture for Armorsmith Extended
+Armorsmith Extended
+Armor and Weapon Keywords Community Resource (AWKCR)
+Caliente's Beautiful Bodies Enhancer -CBBE-
+Merged Fixes
+Looks Menu Customization Compendium
+Companion Stealth Distance Fix (No Free Hugs) - Now with No Dogmeat in Crosshairs
+RAW INPUT - The Ultimate Mouse Sensitivity Fix
+Flicker Fixer ESL v5.6
+Workshop Framework
+Unofficial Fallout 4 Patch
+Crafting Highlight Fix
+Faster Workshop (Workshop Lag Fix)
+PrivateProfileRedirector F4 - Faster game start (INI file cacher)
+Mod Configuration Menu
+Achievements