After cleaning up all the errors around id values in the toc.ncx, epubcheck returned the following:
Code:
main.xhtml 10 338 Col: 61: ERROR(RSC-007): Referenced resource "cover.jpeg" could not be found in the EPUB.
I then looked at the contents of Images where the file was named Cover.jpeg. As mentioned multiple times, case sensitivity matters. On a Linux install, Preview did not show the cover image since the file system is case sensitive. A quick and dirty test on two ereaders (Kobo and Kindle) showed neither would display the cover image unless the case matched (both use Linux as the underlying OS).