Here is my modification of kubrick: http://www.threebadfingers.com. I still need to change use of some IDs to Classes in the right sidebar searchforms.
To convert kubrick to a three column format, I added get_sidebarLeft() and get_sidebarRight() functions to wp-includes/template-functions-general.php. This works great, but I am concerned that this file will be overwritten when upgrading. Is there a better place to define functions within the theme to provide for more modular code?