Your CSS items are not closed:
Code:
<item id="covercss" href="css/cover.css" media-type="text/css">
<item id="css1" href="css/page1.css" media-type="text/css">
<item id="css2" href="css/page2.css" media-type="text/css">
<item id="css3" href="css/page3.css" media-type="text/css">
they should be:
Code:
<item id="covercss" href="css/cover.css" media-type="text/css"/>
<item id="css1" href="css/page1.css" media-type="text/css"/>
<item id="css2" href="css/page2.css" media-type="text/css"/>
<item id="css3" href="css/page3.css" media-type="text/css"/>
This might cause the failure in looking up for ids in manifest from idrefs in spine.