Just out of curiosity if you have and devices which plug in a USB to a wall charger you can just swap that USB to device cord with your kindle cord and it would work.
Now when I couldn't get the mfgtool to register when I pressed magic key I just charged my kindle for a while and tried again and used the tool to reboot into diags using the tool and it worked. Once you get into diags you can then get into usbnet and get into ssh.
From there I used the guide and the 4.0.0 images and everything went great. You should be able to update to 4.1.0 after.