Marker Prototypes File - The one that places visual dots on the map for points of interest.
This wasn't working in the EE so I took a look at the file from main and apparently they changed the UUID format of this file to this type SUBREGION_TradingPost_37e0c493-d738-49bf-957e-024540639cbb. Where as in classic this type: SUBREGION_TradingPost <37e0c493-d738-49bf-957e-024540639cbb> worked perfectly fine. Quick and easy change and now it's working.
Object Scale: For whatever reason Larian decided to change the default size of the Leaves on some trees. So I had to edit all of them in my mod to make them the appropriate scale.
SoundVolumeTriggers - Because of that exceptionally irritating bug in the EE which keeps playing the MAIN menu music in any area that doesn't have an ambient/music resource defined, I had to update all my SoundVolumeTriggers that were supposed to be silent with "Playlist_Mute_Trans" so that the music stops when it's supposed to.
Also I had to add SoundVolumeTriggers to every location otherwise it will start playing the MAIN menu theme.