You've been incredibly helpful and I appreciate it!
After more testing I have a suspicion that the nightstriker mod is the problem, as I found my last good save (only two active scripts) was when Dogmeat was my companion and before I met the companion Nightstriker while my first bad save was after I met the companion Nightstriker and took it along as a companion. But if I terminate that script in the bad save(s), I get a CTD upon trying to load those saves.
I did once uninstall the Nightstriker mod, but because it must've been added to the leveled lists I got attacked by invisible Nightstrikers I couldn't target in VATS. I reinstalled it a few days ago to fix that problem and the mod seems to work as intended... unless it does indeed turn out to be the actual culprit, I guess?
Here is my load order. I am using Vortex. "meatypatch.esp" and "meatypatch-manufacturingsoylent.esp" are personal patchs I have made for a few mods that add in raw meat components, in order to sort it in line with VIS-G rules. Those changes do not use scripts, they don't even use keywords, I just slapped [Raw Meat] in front of their names. The only other edit worth noting is that I modified C.R.O.O.K.S. so that it only adds the armors -- it doesn't touch the leveled lists anymore nor does it have any scripts whatsoever; I basically changed it into a cosmetic mod. I made that change before starting this save so I highly doubt that is the problem.
Fallout4.esm
DLCRobot.esm
DLCworkshop01.esm
DLCCoast.esm
DLCworkshop02.esm
DLCworkshop03.esm
DLCNukaWorld.esm
ccbgsfo4001-pipboy(black).esl
ccbgsfo4016-prey.esl
ccbgsfo4020-powerarmorskin(black).esl
ccbgsfo4023-powerarmorskin(camo02).esl
ccbgsfo4038-horsearmor.esl
ccfrsfo4001-handmadeshotgun.esl
ccgcafo4004-factionws04gun.esl
ccgcafo4007-factionws07hrflames.esl
ccgcafo4008-factionws08inst.esl
ccgcafo4009-factionws09mm.esl
ccgcafo4014-factionas03gun.esl
ccgcafo4017-factionas06inst.esl
ccgcafo4018-factionas07mm.esl
ccgcafo4019-factionas08nuk.esl
ccawnfo4001-brandedattire.esl
ccswkfo4002-pipnuka.esl
ccbgsfo4079-pipvim.esl
ccbgsfo4078-pipreily.esl
ccbgsfo4008-pipgrn.esl
ccbgsfo4009-piporan.esl
ccbgsfo4027-powerarmorskingreen.esl
ccbgsfo4028-powerarmorskinorange.esl
ccbgsfo4048-dovah.esl
ccbgsfo4113-ws_reillysrangers.esl
ccbgsfo4099-as_reillysrangers.esl
ccbgsfo4081-pipphenolresin.esl
cccrsfo4001-pipcoa.esl
ArmorKeywords.esm
AutoUnequipPipboy.esm
CC Handmade Shotgun VIS-G Patch.esl
HUDFramework.esm
I'm A Raider Dammit - Explicit.esl
Region Names on Save Files.esp
Rusty Face Fix.esl
SimSettlements.esm
Sim Settlements VIS-G Patch.esl
WorkshopFramework.esm
SimSettlements_Patch_Nukaworld.esl
TrueStormsFO4.esm
UnderwearCW.esl
tooun_Animationpack.esl
DoYourDamnJobCodsworth.esp
Boston Natural Surroundings.esp
LString_Bow.esp
Better Manufacturing.esp
BetterModDescriptions.esp
PiperCaitCurieDialogueOverhaul.esp
BTInteriors_Project.esp
Better Landscape Grass - Far Harbor.esp
BostonFPSFixAIO.esp
Armorsmith Extended.esp
Better Locational Damage.esp
Immersive_Lexington.esp
BTInt_Optimization.esp
Boston State Prison.esp
BTInt_Optimisation - Region Names Patch.esp
CombatZoneRestored.esp
AA FusionCityRising.esp
RadiantBirdsv05.esp
Reverb and Ambiance Overhaul.esp
SimSettlements_XPAC_Conqueror.esp
LushAmbience.esp
Institute Patch for PRC.esp
DCGuard_Overhaul.esp
Scrappable Red Rocket Pump Arms.esp
SimSettlements_MegaPack_YearTwo.esp
Backpacks of the Commonwealth.esp
Boston Pirate Radio.esp
3DNPC_FO4Settler.esp
ManufacturingExtended.esp
Better Manufacturing - Manufacturing Extended Additions.esp
cartman1975_soylent.esp
Better Manufacturing - Soylent Green Patch.esp
Better Manufacturing - Manufacturing Extended Expanded Patch WO.esp
BOREALIS.esp
BLD - Leveled Lists - DLC.esp
WorthlessMod.esp
BloodMoonRaiders.esp
ArmaliteRifle.esp
AzarPonytailHairstyles.esp
Better Chems - Valdacils Item Sorting.esp
Better Locational Damage - DLC_Automatron.esp
Better Locational Damage - DLC_Nuka_World.esp
RaiderPAChopShop.esp
YogCrowbar.esp
evilzeromerge.esp
Better Locational Damage - DLC_Far_Harbor.esp
Better Locational Damage - DLC_WWorkshop.esp
Better Locational Damage - Valdacil's Item Sorting - Patch.esp
Better Perks - Enhanced.esp
BetterNightVision.esp
C.R.O.O.K.S.esp
CROSS_GoreCrits.esp
CROSS_GoreCrits_FarHarborPatch.esp
Campsite.esp
Chainsaw.esp
CompanionStatus.esp
ConceptCentaur.esp
Crimsomrider's Accessories.esp
DD_flag_poles.esp
TrueStormsFO4-FarHarbor.esp
DarkerNights.esp
MiscHairstyle.esp
The Eyes Of Beauty.esp
FF Cait Dirty.esp
Faded Glory - Soundtrack Expansion.esp
Fixed Alpha Map.esp
Friffy_Holstered Weapons.esp
Handmade Shotgun Fixes.esp
HoloTime.esp
HumanMeat.esp
JUSovietLeathers.esp
LooksMenu Customization Compendium.esp
LooksMenu.esp
VIS-G Item Sorting.esp
MoreNoticeableHitEffect_Hardcore.esp
No more monochrome - Color setting for the Pipboy!.esp
OutfitSwitcher.esp
PRC Patch for Enbs.esp
Project Reality Footsteps FO4.esp
Sarcastic Sneak.esp
SettlementMenuManager.esp
SimSettlements_CityPlanPack_ContestEntries.esp
SimSettlements_XPAC_IndustrialRevolution.esp
Smoke-able Cigars.esp
Swinging Meat Bags.esp
TheFourHorsemenMasks.esp
TrueStormsFO4-EarlierSunsets.esp
TrueStormsFO4-EarlierSunsetsFH.esp
VisibleWeapons.esp
WastelandFashion.esp
WastelandFashionBandanasBlindfolds.esp
bld-racecustomizer.esp
bldvis.esp
humburger.esp
spacefiddle_Follower-Stealth-Distance-Fixes.esp
weedypatch.esp
ProfGood.esp
Transpartent PA Visors.esp
LureEnemies.esp
BetterModDescriptionsAE.esp
3DNPC_FO4Settler_SimSettlements.esp
Floaters.esp
RansackedRelay.esp
AdvancedNeeds2.esp
AzarHolsteredWeapons.esp
DWUK_LexingtonInteriors.esp
CommonwealthCritters - Both DLC.esp
LR_Pizza.esp
SimSettlements_MegaPack_YearOne.esp
WVSimSAddon.esp
Altairp's Animal Farm.esp
Advanced Needs 2 Vis-G.esp
RU556.esp
Survivalist.esp
Bad Dragon Radio.esp
Journal.esp
Balaclava.esp
CommonwealthConifersREDUX.esp
ManufacturingExtendedFH.esp
BOREALIS Grasses.esp
Loot Detector.esp
meatypatch-manufacturingsoylent.esp
KillTips_by_tooun.esp
XM2010_SniperRifle_by_tooun.esp
Craftable Cats.esp
RussianAssaultPack.esp
EnhancedLightsandFX.esp
Pip-Boy Flashlight.esp
StartMeUp.esp
Famished.esp
NightstrikerCreatureMod.esp
RedRocketMCS.esp
Better Landscape Grass.esp
meatypatch.esp