DoubleYou

TexGen currently isn't capable of reading the Next Gen ba2 archives. You can downgrade them with this for now:
 

Either the apps folder is missing from the Bethini Pie install, or the start in directory is incorrect. 

The Step guide requires all the Creation Club mods included in the Anniversary Edition. Not having these will cause the game to crash.

Add this to your Skyrim.ini:
[Bethesda.net] bEnablePlatform=0

Ambient Occlusion checkbox under Detail > Shadows. The pic on Nexus is from older version of the GUI.

My guess is you have SSE FPS Stabilizer. In which case, remove it. 

It crashed loading something to do with facegen, NPC heads. So do a binary search on items that may affect those kinds of things (e.g., High Poly Head).

Install Grass Cache Fixes, place at bottom of load order, generate cache for WhiterunWorld, regenerate DynDOLOD. 

Here's where your thinking is wrong SSE Display Tweaks doesn't modify the ini files to force the windowed mode state. It applies runtime patch to do so, so no matter what is in your ini file, it will be overwritten by SSE Display Tweaks. Disable SSE Display Tweaks, and it should open in windowed mode as expected.

https://www.nexusmods.com/skyrimspecialedition/mods/1778

I would disable the mod providing this texture: textures\pulcharmsolis\kvetchimerc\helmet_n.dds
You might not crash until the mesh comes into view, which is probably why you didn't crash when you visited. 

Vortex uses the default location to store its ini files. Documents/My Games/Fallout 4. Fallout4.ini, Fallout4Prefs.ini, and Fallout4Custom.ini are the ones used by the game, and are the files that will be set to read-only if ticking that option in BethINI under Setup. I personally do not recommend doing so, as it disallows you from permanently altering settings via the in-game menu, such as volume. 
MO2 may or may not use profile-specific ini files, depending on if that setting is turned on for the profile. 

You are not loading from the grass cache. The game is recreating the grass layout every time you visit. Fix your configuration to only load grass from the grass cache using Grass Cache Fixes.

BethINI is designed for the Steam version, not the Xbox version. My guess is there is a file it is looking for that is not present in the Xbox version of the game. 

The uGridsToLoad setting in Fallout4Prefs.ini will override any uGridsToLoad setting in Fallout4.ini and Fallout4Custom.ini. 

You're probably not waiting long enough. Some mods are large compressed files and take a while to extract. Depends on your system too. 

The easiest way to find out what is changed is to view the Summary of Changes before exiting. I would recommend you restore the Before BethINI backup of your INI files to restore it to how it was (Setup tab, Restore Backup, Before BethINI) to ensure that fixes it. Then, when editing with BethINI, you can view the Summary of Changes for anything that it changes, which will help you find out what you need to have in order for it to be correct.

Game settings are not ini settings. Game settings can be changed via console commands or via a plugin. Since you mention a Fallout 4 mod, I assume you want this to apply to that game. Fallout 4 has an ini setting that can be used to enter console commands automatically at startup. 
Fallout4.ini 
[General] sStartingConsoleCommand=bat startup In this example, simply make a text file named startup.txt and place it in the game directory beside Fallout4.exe. Enter in the text file all commands you want to use at startup. 
Be aware that some mods (such as Clarity) have a plugin ini using this method already, in which case you would need to modify it there. 

You are supposed to tick the "HD Grass" option, which is NOT greyed out. The HD Grass option replaces the standard Grass option.

The Fallout4Prefs.ini you found in the game folder is not used by the game. It serves as a baseline INI file for the Fallout 4 Launcher when it creates your INI files.
 
You should also have a Fallout4_Default.ini (I might have the filename slightly wrong) in your game folder that is used by the Launcher as a baseline for the Fallout4.ini file you are having trouble with. Please ensure that file exists and is not blank. If it doesn't, let me know. That would cause your Fallout4.ini to not populate correctly.

Ah. My first computer was a potato too. You could try using BethINI on the Poor preset. Basically, you're going to need to crank everything as far down as you can stand.

I would try re-downloading and reinstalling ENB Light. Could be your download was corrupted. 

It is completely safe to go above 60 fps if you use SSE Display Tweaks. 

Yes. 

Tick the "Remove Grass" button in BethINI.