I have enabled everything to make userChrome.css work, but it doesn't seem like any JS works when I paste it into a userChrome.js file in my chrome folder, including this JS snippet, it could be because I'm on macOS. I should note that the chrome folder is not in my profile directory, its somewhere else and symlinked to that profile and 4 others.
I am on MacOS. I can't help you in regards to the linked profile directory, if you think it needs to be set that way I believe you. But, I did set up userChrome.css the other day and I couldn't get it to work until I went to about:config and toggled the following to True:
Now this is specifically what I did for a userChrome.css not .js but most guides I found only said to toggle toolkit.legacyUserProfileCustomizations.stylesheets but it only worked with those additional flags set to True as well. Maybe this will help you out some.