Well, the latest JB now protects itself from being locked out, and includes a working "su" which KUAL scripts can rely on to escape the user "framework". Also, if you drop a script named emergency.sh into the root of the Kindle Drive it will be run, as root.
So fw5.6.1 no longer goes nuclear on our hacks.
That being said, it is not unreasonable to think some/all hacks need tweaking to run properly -- but they can now be installed.
We need more guinea pigs.
At least nothing catastrophic should happen to these ones.
(Sorry, @pghaworth, for your now-less-than-completely-useful PW2. But it was for a noble cause.
)