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The serial number is found in the image at 0x200. It is zeroed since the image does not know what the serial number of your Kobo is. You can edit the image to place your serial number in the image before imaging but no one has mentioned any issues with having the zeroed serial number.
As for the USB error, try connecting your Kobo and then deleting the bad descriptor. You can use NirSoft's USBDeView to do this as well as Windows Device Manager.
Depending on where you put the books, they will not be recognized. I would suggest a dedicated directory in the root of the exposed partition to place the ebooks into.
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