MusicBrainz Picard is a software for tagging and organising music. It can apply the tags directly to the file and then move them into a folders like Music\Album\01-Song.mp3
An easy way to spot duplicates at that point is search for any songs that have (1) or (2) and so on in the file name.
Then you can use basically any music player to sort by title to check for duplicates, too.