Twine 2 occasionally bungles things up somewhere. If the version in the "Stories" folder is the latest version, import that into Twine, and then you should probably be able to publish that properly.
Regarding playing audio, in some browsers, like Chrome, you need to interact with the page before the audo will work. So you might want to have the audio start after the player clicks an "Unmute" button or on the second passage in the story.
Also, only certain audio formats are supported by various browsers. The MP3 format is probably the safest.
If that doesn't work, it could be the path is wrong. If you're trying to play a local audio file in Twine you'll need to use an absolute path (i.e. "C:/Games/MyGame/Music/Song01.mp3"). If you're trying to play local audio in a published copy, then a relative path is fine (i.e. "Music/Song01.mp3", assuming the HTML file is in "C:/Games/MyGame").
Hope that helps! :-)