I find it funny that the graphic they selected was an iPhone, when the big issues with the Carrier IQ software is on Android phones.
If they are not replacing the screen, just the board, then I think they are wasting their time. Based on how awkward the FreeRunner is with regards to the shape and size of the screen (480x640), they will never be able to compete with any recent Android or iPhone model.
Since they stated it will be using the same case, they are really limiting how much they can do for the FreeRunner.
The downside of this approach is the risk of data leaking onto the unencrypted volume, through temporary files, swap space, browser caches, files inadvertantly saved in the wrong place and so-on.
That's 100% correct if you need plausible deniability, and it is why TrueCrypt recommends using a "Hidden Operating System" or mounting from a live-cd for this kind of protection. While scripting all of what you said above is possible, if you miss one small thing then you can lose your plausible deniability.
If you just want to protect the data and the names of files don't matter, then there are a finite number of places on windows you could clean via scripts out that would clean up any temporary files laying around.
You could try this vibrating bracelet that will vibrate on incoming calls. I don't know if does anything for incoming emails, but it might be worth a shot for $30.
I like the Zagg case that has a keyboard in it.
For taking notes, I like notability, because you can type and draw with a stylus. Also, if you record audio, it can sync up with the drawing/notes you took. This feature is great if you want to listen to the context of the lecture based on your notes.
egrep -n '^[a-z].*\(' $ | sort -t':' +2.0