Ah, I took a look at the standalone content.opf and it has had junk inserted into it by something:
Code:
<item id="index.php" href="Misc/index.php" media-type="text/x-php"/>
<item id="index.txt" href="Misc/index.txt" media-type="text/plain"/>
<item id="part_2_1974.txt" href="Misc/part_2_1974.txt" media-type="text/plain"/>
<item id="w1navigation.php" href="Misc/w1navigation.php" media-type="text/x-php"/>
I copied the nonsense entries and pasted them above.
Epub does not support php files. They are scripts that no epub supports. But something you used to read or edit the epub with probably injected.
Throw out that separate content.opf. Use the .epub file you actually posted.
Start fresh with it.