Ah, I think you've misunderstood how the resources are supposed to be. You shouldn't remove / edit the lines that are already there, because your mod may still depend on some of the stock assets, and if they are no longer within this scope, the game won't find them. Only add new lines for your own mod. It's enough to add only 1 line at the top of your mod's folder name, because AddSubDirs will add everything underneath it.
<Resources>
<Directory Path="/FinalRevelations" AddSubDirs="true" />
<Directory Path="/_temp" AddSubDirs="true" />
<Directory Path="/fonts" AddSubDirs="false" />
<Directory Path="/maps" AddSubDirs="true" />
<Directory Path="/textures" AddSubDirs="true" />
<Directory Path="/models" AddSubDirs="true" />
<Directory Path="/gui" AddSubDirs="true" />
<Directory Path="/static_objects" AddSubDirs="true" />
<Directory Path="/sounds" AddSubDirs="true" />
<Directory Path="/main_menu" AddSubDirs="true" />
<Directory Path="/shaders" AddSubDirs="true" />
<Directory Path="/lights" AddSubDirs="true" />
<Directory Path="/billboards" AddSubDirs="true" />
<Directory Path="/entities" AddSubDirs="true" />
<Directory Path="/graphics" AddSubDirs="true" />
<Directory Path="/viewer" AddSubDirs="true" />
<Directory Path="/particles" AddSubDirs="true" />
<Directory Path="/models" AddSubDirs="true" />
<Directory Path="/music" AddSubDirs="true" />
<Directory Path="/flashbacks" AddSubDirs="true" />
<Directory Path="/textures" AddSubDirs="true" />
<Directory Path="/misc" AddSubDirs="true" />
<Directory Path="/commentary" AddSubDirs="true" />
<Directory Path="/custom_stories" AddSubDirs="true" />
</Resources>
This should fix that. Also make sure that since it's in your mod's root folder, that this is in your main_init.cfg:
Resources = "FinalRevelations/resources.cfg"