How do you know you still have a low battery? That warning screen is left over from when a low battery was detected during startup. MfgTool and fastboot mode do not write to the screen.
<waiting for device> in fastboot could be caused if you have USB problems. You could try a different USB cable, or a different USB port, or a different computer.
If your host PC USB ports are working correctly, you should be able to see the kindle (or USB HID device) VID/PID in device manager property details for that device. In linux, you can use "lsusb" to see attached USB devices. The VID is 0x15a2 for freescale (the CPU SoC manufacturer) or 0x1949 (lab126, the kindle manufacturer). The PID (second number) depends on which mode the kindle is in.
If the MfgTool does not complete, it is usually a low battery condition. It would not start if it did not see a kindle in USB Recovery mode, and it would complete if the battery was charged enough.
A worst-case situation if your battery refuses to charge, is that you could connect to the serial port in the kindle and change to fastboot mode to see the battery charging messages fastboot sends to the serial port. Although unlikely, it *is* possible that your battery is damaged and will not charge, because a bricked kindle can severely deplete the battery.
Do not give up. If you just cannot get the battery to charge (do not trust the LED), try the serial port to see if it is charging in fastboot mode.
Last edited by geekmaster; 03-05-2012 at 10:58 PM.