I'm having battery issues as well. I left the kindle charging on a wall charger overnight, but now I just get the low battery screen no matter what.
When I use the mfgtool, it can successfully detect the connected device as an "HID-compliant device", and when I try to go into either diags or fastboot mode, the progress bar completes and my screen blinks, but it comes right back to the low battery screen, and MfgTool says "Please connect device." until I hard-reboot the kindle again.
If I try to switch to fastboot mode and use yifanlu's kindle fastboot tool, it just hangs on < waiting for device >. Any clues? Is the battery dead, or am I misunderstanding the steps?