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It sounds like a problem with the Kindle. The first error is a permission error with the file metadata.calibre on the Kindle. The second errors I'm not sure about. It could be a corruption on the Kindle.
Try running whatever disk checking tool you have with OS X and see if you can find what the problem is witht he Kindle filesystem. Also, try checking the permissions and finally try moving metadata.calibre off of the Kindle. All of this without Calibre running.
Then you can try Calibre once you have done all this.
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