>those unsorted folders
Get foobar2000, install foo_fileops.dll component.
Add everything in music library to fb2k
Select every file
Sort with the filename pattern %album artist%/%album%/$ifgreater(%totaldiscs%,1,%discnumber%-,)%tracknumber% %title%
Everything is mostly sorted. I think my brother did some shit a while ago though when he took my external to school to transfer some files or something because he's too cool to use a USB.
A lot of the songs I would listen to are gone though, and my playlists completely broken. So I figured I'd just wait until my lazy ass finds a good place to download until I fix everything again. Besides, what I do still have is sorted in foobar itself which is mostly all I care about atm.