Custom Entities

[Your Computer]

lol. Are you hinting that it is as simple as inserting the custom stories folder in the default resource file?
Edit: because then I would do that.

When you add the custom_stories folder to the original resources.cfg file, the level editor will no longer remove custom entities or objects when loading a map (e.g. "File index out of bounds") (obviously assuming your story's resources are located in that directory). The only thing adding the custom_stories folder to the original resources.cfg doesn't do is have your custom resources listed among the others, but that's a non-issue.