Plex can’t read tags from WAV files. Try converting the files to FLAC.
The second thing I see, from the log snippet it appears that your files don’t actually have the track number in the filename. That actually shouldn’t be a problem for Plex - it’s just different than you mentioned earlier.
I strongly recommend not including the disc number in the filename. In my experience, Plex does best if the filename is “xx - track title.flac” where “xx” is the track number only. The track number can be “1, 2, 3, etc.” or (my preference, so the OS will sort them properly) “01, 02, 03, etc.”
If Plex is fully configured to prefer embedded tags, it’s fine to have them in the album folder itself, or in ‘Disc x’ sub-folders. Plex does fine either way.
I’ve never used the “~” character in a folder or file name, and I have no idea if Plex has any problem with that. If none of the above suggestions resolve the issue, you might try replacing tildes with square brackets [ ].
