You answered your own question.
The process you used, save to disk, copy to device, connect CC, scan for new books; depends on the book having sufficient embedded metadata for calibre to match the book on the device to the library. Reason: neither CC nor calibre know where the book came from. As far as they are concerned the books fell out of the sky. In your case, it appears that calibre could not match the books, so they ended up with being named as you described.
The correct process is connect CC as a wireless device and send the book from calibre, or (as you discovered) connect to the content server and pull the book to the device.
There are two ways for you to fix this.
1) Connect as a wireless device, switch to the device view, find one of the unmatched books (the "In Library" column will not be checked). Right-click on the book and choose "Match book to library". Enter the correct title (the one in the calibre library) into the search box, press search, and choose the right book. You might want to note which number is which book before starting this process.
2) Delete the books from CC, connect as a wireless device, and resend them from calibre. You can do this in one calibre operation. Yes, it might take a while, but you don't need to watch it. And in any event, it might actually be faster than matching the books individually.