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It does sound like your two error messages come from the same problem. And that problem is not listing all of your content files in the .opf file.
You mention constructing the toc.ncx file, but you also need to make sure that all content files are listed in the <manifest> in the .opf (which can vary in name and location and is named explicitly in the META-INF/container.xml file).
Then additionally you need to list a reference to each 'content' file in order in the <spine> in the .opf file. That reference uses unique id you gave it in the manifest entry. The spine is what tells book readers what files show in what order.
I suggest examining the contents of the .opf file for a few epubs and reading the epub standard about manifest and spine.
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