One annoying that Sigil does is messing with the file structure. All .html files end up in the Text folder, all images in the Images folder etc.
Therefore, you'll need to prefix file names in the guide
section with Text\
. I.e., they must have the same path as in the manifest
section. For example:
<reference href="Text/SpringCover.html" title="Cover" type="cover" />
<reference href="Text/contents_and_statement.html" title="Table Of Contents" type="toc" />
As for the cover page, KindleGen ignores it, if it finds an <image> tag. Simply add semantics to the cover image.