Your folder structure is still a bit off; you should not have either of the Episodes or Shorts and Specials directories. And all of your specials should be either in a directory named Season 00 or Specials, with no sub-directories. The documentation provides a very good example at the bottom of the page:
https://support.plex.tv/articles/naming-and-organizing-your-tv-show-files/
And, after correcting your naming and directory structure, you may have to perform the steps described here (Plex Dance):
