I never posted an update to this so I'll do it now just so that the thread has some closure.
I have continued using Calibre, most of my problems stemmed from having side-loaded books that Calibre identified as being both in the library and on the device, so it never sent them and for some reason updating metadata wasn't working. I simply removed all of my side-loaded epubs from the device and told Calibre to send everything over, the KoboTouchExtended plugin kicked in so now I have a library of kobo epubs on my device with nice full titles and a fair bit of information (I downloaded a lot of metadata so it updated very nicely).
I'm faced with a bit of a problem when it comes to updating the covers and getting them to look the same, the problem is detailed here -
https://www.mobileread.com/forums/sho...90#post3188290
So far so good on everything else. Managing ebooks with Calibre turned out fairly easy, now I need to add series information to everything so that things get clumped up in nice convenient collections on the device. That and fix my cover issue so that my lock screen looks nice and shiny rather then blurry and pixely.