So far the MBWE has proven to be a great and cheap NAS with room for expansion. The current method for adding programs demands installing from source, but tracking down dependencies is not always easy. What if we could gain the simplicity of the Gentoo Portage system? Is there an "easy" way to "Gentooize" my system so I can just emerge {program} and be done with tracing dependencies forever?

Starting with what I've learned thus far at http://mybookworld.wikidot.com/ I think there is quite a good possibility of doing so.
The first and most crucial step is to gain SSH access to your MBWE. After that we need to get the heart of Gentoo working, which is Portage.