Alright boys and girls, I spent some time tinkering with this tonight and found a solution using user preferences. I am considering writing a zenity front-end/(python/bash) backend to automate user input, bridging or to replacing "alacarte/Main Menu" functionalities to make this easier for the average user.
Here is what I have found so far ->
1) User customization is based in ~/.gconf/desktop/unity/launcher/favorites
2) Each application in your favorites has a directory within the favorites folder, and is indexed/referenced using the %gconf.xml
3) If you have already created a custom folder/application using alacarte/Main Menu, you should already have a file created under /usr/share/applications you can reference in the next step. Otherwise, make one using alacarte/Main Menu
4) cp -pr ~/.gconf/desktop/unity/launcher/favorites/app-firefox.desktop ~/.gconf/desktop/unity/launcher/favorites/app-[custom_name].desktop
6) vi ~/.gconf/desktop/unity/launcher/favorites/app-[custom_name].desktop/%gconf.xml
7) insert a line like so (inside the <gconf></gconf>):
<entry name="desktop_file" type="string">
</entry>8) Logout and log back in, or restart gdm ('sudo restart gdm')
NOTE: I assume similar things can be done to add programs into "Applications", but I expect it will live under /usr/share and effect ALL users...
Have fun! I will post back here when/if I create the GUI front-end to handle these steps, and provide a method to retrieve the .deb package