I think you are so close to making it work. I wish I could look at your system and say exactly what steps you should take. I agree that the transition is harder than it needs to be because the process is brittle.
ALL of my previous V5 shortcuts got changed to V6 shortcuts; even my personal CUSTOM V5 shortcut.
If one does a search, I did create a few posts on how libraries worked between operating systems. At this point in time, it appears that OS upgrades changed some of these things (and it should NOT).
I had similar problem going from V5.1 to V6.0. I made it work (on ?Ubuntu 20.04) using Preferences - Configure paths, then click “+” to add “KICAD_FOOTPRINT_DIR” (notice the 6 isn’t there) and the proper directory, repeat for “KICAD_SYMBOL_DIR”. Add “KISYS3DMOD” and the dir for 3D models.
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