Updated: April 24, 2019
Credits to igloo4#9768 on Discord for the initial write up
Open up Shoko Server if it is not already open. Then, open Shoko Desktop.
In Settings > Users Type your plex username in the “Plex Users” field Click “Save", then click “Link To Plex”
A small window should pop up. In the new little window, click “Link", then click the hyperlink “Click here to log in” The link should take you to plex, asking for permission to share libraries with shoko. Login and accept.
Go back to the small window. Where they hyperlink was, it should now say “Done”
Open Plex and create your new anime library (I'd recommend at least one library for series and one for movies)
In the advanced tab of the “Add Library” popup, set Scanner to “Shoko Series Scanner", and set Agent to “ShokoTV” or “ShokoMovies” (depends on the library type) Scroll down to see the new ShokoMovies/ShokoTV settings
Enter your Shoko username (found in Shoko Desktop: Settings > Users) and password (if you do not have one, leave this field blank) Enter the IP and Port information found in Shoko Desktop: Settings > Essential
Click the big orange “Add Library” button
Repeat this step for as many libraries as you would like to create.
Once Plex has finished creating your libraries (once the orange spinning bars in the top right disappear), shut down plex. Then, shutdown Shoko Server >Make sure both are actually closed, not just minimized to the system tray (notification area)
Start Shoko Server, then start Plex and Shoko Desktop
In Shoko Desktop: Settings > Essential, at the very bottom of the page, you will find Plex Settings for ShokoMetadata
Follow the instructions there to find your Plex Host and Plex Library IDs.