The problem with replacing scripts is that they are listed in the game resources ('Data\Public\Main\Content\Assets\Scripts' and '...Shared\Content\Assets\Scripts') with a unique ID and a folder location. If they're stored at a different location they'll get ignored.
The Base script, for example, is listed in 'Data\Public\Shared\Content\Assets\Scripts\[PAK]_Base\Base.lsb' with the following information:
<node id="Resource">
<attribute id="ID" value="ed3701ac-8b42-4ba9-b92f-6273a6f6b525" type="22" />
<attribute id="Localized" value="False" type="19" />
<attribute id="MapKey" value="ed3701ac-8b42-4ba9-b92f-6273a6f6b525" type="22" />
<attribute id="Name" value="Base" type="23" />
<attribute id="SourceFile" value="Public/Shared/Scripts/Base.charScript" type="30" />
<children>
I had the same problem with my current mod project. There are two options:
1. Very inefficient: Adding the new versions of your scipts to the resources of your mod via Resource Manager and re-assigning them to all related characters (i. e. replacing the old script IDs in the character information with the new ones).
2. Best option (that's also what XC_Bags does): Adding the new version of the script to the resources of your mod via Resource Manager (the file will be in 'Data\Public\YourMod\Content' or a subfolder of the 'Content' folder, depending on what structure you create), converting the lsb file in your 'Content' folder to lsx with Norbyte's tool, converting the 'Base.lsb' from 'Public\Shared' to lsx, opening both lsx files with a text editor and replacing the ID and MapKey of the 'Base' script in your lsx with the original ID and MapKey in 'Base.lsx', and converting your file back to lsb.
If you have a great amount of scripts to replace you can also copy the relevant content lsbs of the main campaign to your content folder and just replace the location information (Shared or Main) with the script location of YourMod.
Edit: Unfortunately the 'Copy to my mod'-function of the Resource Manager still locates the script in Main or Shared (checked it in the content lsb of my mod), not YourMod, which makes it quite useless.
