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Installing MO2 for Fallout 4 - beta issues



The above link is to the Forum for the Guide.
There is a link to the Guide in the 1st Post at the top.
Have fun modding and I hope this helps you all.
[spoiler=OLD POST INFO]
Installing ModOrginizer 2
beta 3
This is to avoid some issues and bugs that are occurring atm
-Issue MO2 not starting after the 1st run.
-Issue profiles are unreachable or incomplete file structure in them once symbolic link created functions normally
-Issue overwrite folder in MO not showing files that are in the Directory
-Loot not showing more than main and DLC files
NOTE: IF you are using NMM and just trying this out then you will in most likelihood have unexpected results, you need to start with a clean installation of FO4 to reduce the chance of errors. You could zip up your FO4 install folder then reinstall FO4 (if you want to revert to NMM). This will give your best chance, NMM leaves bit's and pieces everywhere and uninstalling mods from NMM is not good enough.
My recommended installation
> Install MO2 (Change to C:\ModOrginizer2)
> Add the C:\ModOrginizer2 folder to Windows Defender Exclusions
> make  ModOrganizer.exe run as an Administrator
[spoiler=Installing ModOrginizer 2.0.7 beta 3 (with Profiles)]
> make a Folder C:\ModOrginizer2Data 
> Move the Contents of the Mod Organizer folder from C:\Users\{User}\AppData\ModOrganizer to C:\ModOrginizer2Data
> Open an administrative command prompt, then create a symbolic link with the following command "mklink /J C:\Users\{User}\AppData\Local\ModOrganizer C:\ModOrginizer2Data" You do this so the overwrites folder works.
> Go into MO2 Settings and in the NEXUS tab enter your login Information.
NOTE 1:To resolve download manager issue from Nexusmod site I recommend deleting the nxmhandler.ini from C:\ModOrginizer2 and C:\ModOrginizer2Data then run nxmhandler.exe in MO2 root folder to generate the nxmhandlers.ini files
NOTE 2:If you have issues with your profiles you can try (make sure you backup) deleting C:\ModOrginizer2Data\Falout4\ModOrganizer.ini when you restart MO2 it will remake it.

[spoiler=Reset and Clean config Files]
MO2 appears to not manage your ini files and ini mods SHOULD go in your Fallout4Custom.ini it would be nice if this becomes a thing in MO2 but for now please do the following.

Backup your Fallout4.ini and Fallout4Prefs.ini 

run fINIp4 follow the instructions, it's easy.

Check Fallout4Custom.ini (in \My Documents\My Games\Fallout 4\) has the following lines






I personally use 




The reason for this is that I was not seeing all loose files in mods so some textures were missing and found this resolved that problem. It may be a placebo but It works for me.


[spoiler=How to install F4SE]
Download F4SE Manually and Copy f4se_1_6_3.dll, f4se_loader.exe, and f4se_steam_loader.dll to your Fallout installation folder do not install via MO2
If you want use  Achievements patch  install it with MO2 NOT MANUALLY IN FO4 Directory

[spoiler=LOOT]Install LOOT via the installer (Default settings and folder) If you want extra fun the nightlies are HERE Just copy over the top

[spoiler=FO4Edit]Download Fo4Edit Extract the contents into a folder, rename the TES5Edit.exe to FO4Edit.exe. In MO2 under "modify Executables" Add FO4Edit under title and point to the Binary you just renamed.  

To manage My ENB's i use ENB FXAA SweetFX Manager and Remover The newer ENB Presets seem to be quite complex as they are not fully packaged and This will help you clean out your FO4 if you Muck it up.

e.g. VOGUE ENB uses a LUT's folder in \Data\textures\effects\LUTs if you want to BACKUP these Newer ENB's you need to click files in the top right of ENB Manager,click files and add Data\textures\effects\LUTs to the bottom of the list that pops up.

ENB Manager will ONLY Backup files in that list if you use and exotic ENB with odd files make sure you add the folders( and files if in the root directory) it needs to backup.


Note 1: If your in game light sources flicker on and off when looking around make sure UsePatchSpeedhackWithoutGraphics=false otherwise set it to true
This >>>guy<<< seems to have most informative install video, IMO. His other videos will take you through a lot of advance setting. Worth a look.

Renaming folder should work generating new empty mode requires refresh to show up.
Bodyslide works
F4SE works : it gets Autodetectd By MO2 Dont manually create an executable.
FO4Edit works - generates file in overwrite and mod can be created
LOOT works : it gets Autodetectd By MO2 Dont manually create an executable.
If you use this guide to set things up please NOTE that using Fallout4 ini managers may not function as expected due to Fallout4Custom.ini overwriting most settings. I do not recommend it unless anyone knows of one that mods the Custom.ini with the caveats in this >>post<< but adhering to fINIp4 layout.
To push the install with multiple mods I used a lot of the following mods Ultimate Fallout 4 Compilation They seem quite active.
I hope this helps people out there that want to play with MO2 beta 3 in it's current state, if you have other issues please post on https://github.com/TanninOne/modorganizer/issues  so this excellent work can continue.
I'll update when I get issues and add their resolution.
> Move the Mod Organizer folder from C:\Users{User}\AppData to a new location (in my case j:\{My new folder} on my My 2nd Hdd)
> Open an administrative command prompt, then create a symbolic link with the following command "mklink /J C:\Users{User}\AppData\Local\ModOrganizer J:/{My new folder}
To resolve download manager issue from Nexusmod site I recommend deleting all nxmhandler.ini and ModOrganizer.ini and allow MO2 to recreate them also run nxmhandler.exe in MO2 root folder to generate the nxmhandlers.ini files 
For ENB management I use ENB FXAA SweetFX Manager and Remover
If you want to use FINIp 4 you have to install it them manually copy the ini files into your working profile (Remember to backup)"

MO2 creates a c:\Progam folder on my HDD on WIN 10 you get a popup error when you login - May be just my system. No harm no foul

Edited by Gernash
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I don't need no stinking Symbolic link.....


As far as I've seen it won't work reliably with out it.
You can test for the problem, create a new profile then try to change the paths(under settings), individual paths will reset to %base_dir% and if you change base dir then MO2 will freeze on startup also ini files will go missing in your profile.
Delete ModOrganizer.ini if your MO2 wont start after playing with it. (This will remove Mod activation and Mod order)
Using the symbolic link means you can have your data and profiles anywhere without changing the settings in MO2.
Highly recommend doing it even if installing on a single Hdd (for MO2 2.0.7 beta 3)
Edited by Gernash
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I'm just providing a reference for others for Beta 3 the git hub "feels" like a I have found this bug/issue here is what I experienced. I feel "Dirty" using it for How to/workarounds.

Edited by Gernash
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Manual ordering - not using LOOT


Make sure sort by priority is on

look in the Left pane, the little lightning bolt with + or - 

- has something overwritten

+ overwrites everything above it


If you select one of these mods and scroll through your modlist you will see other mods in highlight in green, they are being overwritten in some way by this mod. Any highlighted in red are overwriting the mod you selected.(Group/Drag these one together in the order of overwrite you prefer.)


Group all your mods 


Unofficial Fallout 4 Patch

Armor and Weapons Keyword Community Resource

{Settler mods}

Settlement Keywords Expanded


then all your Textures or Meshes


then all your Weather mods


then Player mods - like cbbe, body textures clothing


then ui and gameplay


when you see a -lightning double click go to conflicts tab, if the mod you have selected is being overwritten by what you want then all good otherwise drag it below the offending mod. Try to keep all the mods that overwrite each other together. It will keep you sane.



Caliente's Beautiful Bodies Enhancer -CBBE-

Caliente's Beautiful Bodies Enhancer -outfits-

Additional Body Textures - Ghouls and Old people

Vault Booty 1.0.4eaw Experimental Atomic Wedgie


so in that example the Vault Booty overwrites the CBBE vault Suit Ghouls and Old people look like they are supposed to and CBBE gets it updated clothing pack.


To keep things ordered (visually) I create empty mods (that are not enabled) and I name them appropriately, then move the mods under them.


In the left pane click create backup

then click the sort box

everything should now sort and locked mods migrated to the top this delets the plugins.txt

i.e. Keywords, homemaker, robot defense, snap and build basically things in italics move them to the top

then Unofficial Fallout 4 Patch

then your other esp files


Only thing else you can check for is in the data tab, things in highlighted red. They they are esp's being overwritten by some mod. If you hover the mouse over them it will tell you which mod is doing it and you can verify in the left pane if that is the correct overwrite, If not you have to move the mods in the Left pane to change the overwrite order.

Edited by Gernash
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Now that the basics are setup.....




Fire it up and make sure all the esp's you are running are selected.

If it bombs out read the right pane for the error and move the mods accordingly 

usually something like Exception: "Whatever.esp" requires master "Whatever.esm" to be loaded before it


Once you get the order right then all the mods should appear.


You can right click on them then apply filter (default settings) then you will SEE the exact overwrites.


e.g. I use Bobble Girl, Functional displays and Valdacil's Item Sorting


Functional displays >overwrites > BobbleGirl.esp > Valdacil's Item Sorting reverts the Model

So to get Bobble girl to work I drilled down BobbleGirl and did the appropriate edits to an over write mod.


Manual mod merging and leveled item lists >>Video<<

Leveled item Bash patching >>Video<<


Here is a LINK to a video showing how it's done (man he can type;)


If there is a S.T.E.P video detailing this procedure of creating overwrite mods please tell me so I can link it aswell

Edited by Gernash
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