Instead of a full Restore Standard Fonts, all you have to do is disable any fonts that have any characters in their name not in the following list:
In my case, I had fonts with * and + symbols in their name. Disabling those fonts and restarting Sketch allowed me to customize the theme font families through the plugin again.
If that doesn't help, check Console.app under
~/Library/Logs/com.bohemiancoding.sketch3/Plugin Log.log to see what the error is.