MKVmetaclean VS Kitana

https://github.com/cyberbrix/MKVmetaclean for reference

Look into Kitana.

The Plex-Trakt-Scrobbler does this. You'll need the Kitana Plex plugin web frontend to access Plex-Trakt-Scrobbler's UI.

the old plex trakt plugin still works for me, need to use https://github.com/pannal/Kitana to access the the old interface however.

There is also an addon for plex that gives you more control, plex trakt scrobbler. Sadly plex has mostly done away with addons (I think that is why the addon is mostly unmaintained) so I use kitana to manage addons. trakt-for-plex may also be useful.

You need Kitana to access your Plex plugins.

2) Pair it with Kitana to access the web gui.

With kitana 'https://github.com/pannal/Kitana' you can run manual push/pull syncs. Along with more control over other plex plugins.

It still works! You just can't get to plugin GUIs anymore through the Plex app. You can run Kitana (https://github.com/pannal/Kitana) for this though

Did you set the sync to run at a lower interval? Or maybe to not wait until the server is idle? You can also try a manual sync and check the messages see if it returns any errors. The only way to do that is through Kitana after Plex got rid of the plugin interfaces. I run my own public instance at https://kitana.bas.sh if you want to use it.