I suggest sending your mobi files by email, that will cause amazon to assign them a dedicated asin and syncing should then work. The downside is that the books will be listed as personal docs instead of books on your devices.
As for Nexus 4, calibre should already support it if you're on windows. If you're on liunx, you will need to post the usb ids of the device so they can be added to the MTP driver.
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