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It sounds like your kindle is working again (not totally dead) after the battery charged. The jailbreak does not do anything but add an extra key file to ALLOW you to install other hacks. There is really no need to remove the jailbreak.
What version firwmare do you have? The new 5.1.0 has some code for rotation, and the autorotate hack might be conflicting with that. I do not know how old hacks and brand new firmware interact.
The easiest thing to do is install an old mmcblk0p1 for v5.0.0 (using dd from an ssh shell, or dd from a RUNME.sh script), as described in the debricking threads. And the "needs repair" probably needs the boot counter reset, or mmcblk0p3 partially zeroed out.
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