Hi OP - I seem to have created a nightmare. I initially rooted my nieces Kindle shortly after christmas with no issues whatsoever using your guide. Shortly thereafter Amazon released an update that overwrote my changes (why oh why didn't i kill otacerts) and she returned it to me to re-mod. My second attempt was cut short - I hadn't made the contents of Bin4ry or Qemu folders executable and was running into permission denied errors when attempting to execute adb from within the script... after i realized my failure and got access to the device again (tonight) I again attempted to execute the scripts... and bumped into a new troublesome issue... I executed Bin4ry's script and the device rebooted when expected, albeit slowly. I then got to the point where the kindle was flickering the script asked me to unlock the device, which i could do, though responsiveness was slow, and hung on the message saying 'waiting for device to reappear'... it stayed here for well over 20 minutes. I ended up CTRL-C ing that window and tried to find the device using adb devices, but adb was non-responsive. adb kill-server hung as well, so i rebooted my PC and tried adb devices, the kindle is visible (yay!) and i can gain access to the shell, however, and here's my problem, whenever I plug the Kindle into my PC and launch adb shell my PC freezes and I have to power-off and restart. Every time, no matter what.
The kindle is half-way rooted (maybe less) and in a non-operable state... and I can't seem to keep my OS stable long enough to finish... what is going on here? I have to take her home now, am thinking I should try and run the Bin4ry script again but am concerned that my PC may freeze again...
I am updating the SDK as I type, hoping someone more comfortable with the kindles can chime in and lend me some direction, this thing makes me nervous.
ps - ubuntu 12.10 32bit
1 x G1
2 x Sensation
2 x Galaxy Nexus w/ PA4
1 x Samsung Galaxy Tab Plus 7"