In order to run customized tools into the Kindle we will need to know the OS that is running and how to get into it. I suspect that it will run a light version of Linux under an unprivileged user. I updated my Kindle so I get use play with my old one :-]
The following phases illustrate how the process should look like:
PHASE I — Discovery & Research (What's a kindle? What runs inside it? Can we break in?)
PHASE II — Elevating privileges — from reader to super-admin
PHASE III — Compiling or necessary arsenal of tools for security testing
PHASE IV — Perform security tests with it — it will be slow but at least the battery can last for a long time :-]
PHASE V — Document the process