[KevinH]

Yes, the manifest order is meaningless and can never be seen by a reader of the epub. The spine determines the display order by providing an ordered list of manifest ids.

And understand that the manifest will include many resources not part of any one xhtml file such as images, css, fonts, and therefore not part of the spine. So what "order" would you use for those?

If you use Sigil or Calibre, epubcheck can be used and the error information from the validation window will take you directly to the file with the error, and drag, and drop can be used to reorder the spine. And of course using Find when editing the OPF can be used to track down manifest entries if you have really large manifest.