Is there any way to select a song with multiple instances and find out what playlists it is in?

No. If I can figure out a good way to implement it, then there will be.

As a quick hack, you can delete the track completely. This'll mark the playlist as changed. You can then find the playlist by typing 'changed' into the advanced search dialog. Not much help if your playlist is named 'Disc 1', but it might help.