https://support.plex.tv/articles/201370363-move-an-install-to-another-system/
shows you how to do that without losing any metadata.
As you’re having issues with metatdata retrieval, and you’re verging on reinstall from scratch,
I think it’s worth correctly naming at least a few series that don’t work, and doing The Plex Dance with them. Your names aren’t even close to spec on a bunch of series it’s scanning, but naming is incredibly important: https://support.plex.tv/articles/#cat-your-media
C’mon you named an episode 01.mkv. What do you expect to happen 
Custom artwork gets placed inside the TV series directory it’s for. You wouldn’t lose that if you move the whole TV Series directory out of the way during The Plex Dance. The special tags you made, those would be sacrificed. Try doing it for a less important but problematic show maybe?
Let us know how it goes 
