Good. Thank you. That confirms all your media is accounted for and why “TV Shows” and “Movies” exists. 
Given everything seems to be where it belongs,
If I am understanding your symptoms correctly, all which remains to do is grant permissions to your “/Media” shared folder and extend those permissions recursively into that shared folder to grab all your files in one shot.
In the same spirit FAQ 19 is written for DSM 6, we only need change the name to PlexMediaServer for DSM 7.
The rest of the procedure remains unchanged
You will perform this on your master /Media shared folder.
At the end of the FAQ, please take note of “Apply to this folder , sub-folders and files”.
It’s important that all your media , down in the nested sub-folders, are all visible to PlexMediaServer.
Sound easy?
