Cannot get some Mods to work in Skyrim

[cblackstone]

I have NMM, LOOT, and TES5Edit installed and my list of mods here: GameMode=Skyrim

Skyrim.esm=1

Update.esm=1

Unofficial Skyrim Patch.esp=1

Dawnguard.esm=1

Unofficial Dawnguard Patch.esp=1

HearthFires.esm=1

Unofficial Hearthfire Patch.esp=1

Dragonborn.esm=1

Unofficial Dragonborn Patch.esp=1

Falskaar.esm=1

ApachiiHair.esm=1

ClimatesOfTamriel.esm=1

HighResTexturePack01.esp=1

HighResTexturePack02.esp=1

HighResTexturePack03.esp=1

Unofficial High Resolution Patch.esp=1

moonpath_tp.esp=0

Better Dynamic Snow.esp=1

SkyRe_Main.esp=1

Immersive Weapons.esp=1

Realistic Lighting Overhaul - Dungeons.esp=1

Realistic Lighting Overhaul - Major City Exteriors.esp=1

Realistic Lighting Overhaul - Major City Interiors.esp=1

Realistic Lighting Overhaul - Dawnguard Interiors.esp=1

Weathered Road Signs.esp=1

SkyRe_EncounterZones.esp=1

Hothtrooper44_ArmorCompilation.esp=1

WATER DG + DB.esp=1

Cloaks.esp=1

SMIM-Merged-All.esp=1

Farm Animals_HF.esp=1

SkyRe_EnemyScaling.esp=1

SkyRe_Races.esp=1

Catsofskyrim.esp=1

dD - Enhanced Blood Main.esp=1

dD-Dragonborn-Dawnguard-EBT Patch.esp=1

SkyRe_EnemyAI.esp=1

WATER Plants.esp=1

Dogsofskyrim.esp=1

Footprints.esp=1

Hothtrooper44_Armor_Ecksstra.esp=1

Moss Rocks.esp=1

RaceMenu.esp=1

RaceMenuPlugin.esp=1

Realistic Lighting Overhaul - Minor Cities and Town Interiors.esp=1

SkyRe_Combat.esp=1

SkyUI.esp=1

The Dance of Death - Ultimate Edition.esp=1

TheEyesOfBeauty.esp=1

WATER.esp=1

WATER Falskaar.esp=1

WetandCold.esp=1

Alternate Start - Live Another Life.esp=1

ReProccer.esp=1

In NMM there are no conflicting issues and the game starts just fine, however only a handful of Mods show up in the Mod menu in game and are Footprints, Immersive Armor, Enhanced Blood, SKUI, Wet and Cold, and the Dance of Death.

I have only 32 mods and there are ones like Immersive weapons, pets, farm animals, cloaks, etc that are neither showing up in game nor in the mod menu when i pause the game. I am indeed launching in the SKSE format and when I run LOOT it says there are no issues conflicting but most of my priorities are either 0 or -9999xxxx

Here are both my LOOT order view as well as my NMM view