I wouldn't say it's a bad idea... Note that for GUI applications, there's a bit more to "porting" than just compiling the application as-is for the Kindle. You will also need to make the parts that output graphics aware that they are rendering to an e-ink display. The main difference to "usual" framebuffer output is that you have to tell the display explicitly to refresh changed parts of the visual output - it's a display that doesn't constantly refresh.
Personally, I didn't take a look at the sources, but there's
a recent thread about a DirectFB/WebKit/GTK+ bundle - however, since you're targeting the K3, I think those should already be in place.
And yes, you should focus on "missing libraries"... You'll just need them to run the app, it's this simple.
However, there might be another way: You could use a full-fledged Debian installation as a base (search this forum on how to do this). This would spare you of the work to compile all that stuff, and you could focus on the e-ink problem.
Besides the mentioned output speciality, also the input will probably need a bit of work, too. The keyboard isn't quite the "standard PC" stuff.