Man, I never thought that I was playing the game with the spawning issue. Now that I know it's happening, I cant unsee it. I spent 2 days testing my mods. And finally I have managed to have a working game with no spawning issue, at least for me in Valentine. Im still early on Chapter 2 so I still havent gone to St.Denis, but I can confirm that the train is spawning every 6am in Valenting with 3-4 passengers in every car, with guards at the end. There's abundant of wildlife too.
Here is my modlist in lml in its specific order:
Model 1897 Trench Gun
Contracts
MarlboroCigarettes
Upscaled Gore (I use the replacement method)
Mike Myers
Online Alligators Unlocked for SP
Online Bears Unlocked for SP
Online Bison Unlocked for SP
Online Bucks Unlocked for SP
Online Cougars Unlocked for SP
Online Coyotes Unlocked for SP
Online Foxes Unlocked for SP
Online Panthers Unlocked for SP
Online Wild Boars Unlocked for SP
Online Wolves Unlocked for SP
Cut Content Deer Unlocked for SP
Cut Content Dogs Unlocked for SP
ColorfulWeaponsIcons
Corpse Spawn Distance
Gun_Metal_Rework
Herbalist
Hunstman
Jail_Break_Fix_Restoration
Anatomical Women Bodies Fix
NoRecoil
no auto ammo pickup
RemoveExplosionShake
Realistic Accuracy
Saving Spoon Fix
Maize Sack Fix
Remove Online Button
ColoredLoading
Elegant Gamepad Button Icon
NoPostFX
SnappyUI
ManualPickup
Green Turtle Restored
Promo Image Graphics
WhyEm's BloodCrave
ImprovementsInBlood
Timescale
Standalone Landing Screen Edition
A.R.E.P
Extended Player Animations
Vomit Fix
AMFAO
Penetration
More Perfect Animals
Restored Ped Dialogue
LAW
RWS
AB10 (the experimental gameconfig.xml that perhaps fix the spawning issue)
Improved Wildlife
Online Content Unlocker
Geometry Level of detail slider
I got WhyEm's DLC installed in lml, but currently disabled. I noticed if I enabled WhyEm's DLC, I dont get the spawning issue, but only if I dont use any of its items. I tried to apply the WhyEm's DLC Hairdos and it suddenly triggered the spawning issue. So I leave it disabled.
I got Vestigia mod too, but in my test, it triggered the spawning issue even with the WhyEm's DLC disabled. So I switch to Promo Image Graphics. I tried Visual Redemption but I got random crashes with it.
I also have a stream folder in lml with lots of texture files on it, but it doesnt affect the spawning issue. It contains character retex, horse coats, player jacket retex and among others.
I tried installing Upscaled Animals AIO with the replacement method and immediately triggered the spawning issue.
I got a lot of .asi files installed too, but it doesnt seem to affect the spawning issue. If any one wants a list of my .asi files, just ask.
Hope this helps in isolating the mods that may or may not affect the spawning issue.