For MP3 files, synced lyrics are embedded in the SYLT tag. Unfortunately, not many music players support this across platforms.
That could be the case. I used ffprobe to see the tags and figured it would just display the tags it sees. I'll look more into it.
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.