I suppose it is possible that your persistent user store (/dev/mmcblk0p3 mounted on /var/local) is full. You could try zeroing it out and rebooting, so it gets rebuilt. That will delete your collections and settings, making your kindle look "fresh out of the box".
If you want to flash main (and perhaps the matching kernel), the 4.0.1 versions are in the pastebin MIRRORS in the first post of the "simple debricking" sticky thread.
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