I would suggest looking at several working epub3 files with audio (see
A Christmas Carol audiobook for example). Overall, your method of using InDesign and then trying to manually add files is simply asking for errors.
Running epubcheck on your epub came up with multiple errors, most of which were due to having files manually deleted from the epub but a couple were more severe such as the missing media-overlay attribute:
Code:
OEBPS/content.opf 17 1090 Col: 97: ERROR(MED_010): EPUB Content Documents referenced from a Media Overlay must specify the "media-overlay" attribute.
OEBPS/toc.xhtml 9 245 Col: 9: ERROR(RSC-005): Error while parsing file: element "ol" incomplete; missing required element "li"