Hi folks, apparently the forums here aren't sending notifications for your posts, so I'm only seeing this today (thanks to a + from Jerry on Google+).
For the code that built the v0.3 files, you can start from a clone of my repo https://github.com/gregrebholz/Marlin and checkout commit 95c6a2e (from the command line that would be "git checkout 95c6a2e"). This is the last commit before I submitted the pull request to Marlin. From there commits were made to adjust to their requests, and that included a hastily put together Configuration.h that has not actually been used yet on RBCE builds.
As far as EEPROM support, I've been doing the builds by running example_configurations/rigidbot/makeallrigidbots.sh (on a Mac but should work from Linux as well)... it's a very simple shell script that uses 'sed' to search and replace various strings in the Configuration.h file to build the 8 permutations of RBCE posted here in a repeatable fashion. It should have been setting the correct EEPROM values, but I'm hearing from others that it isn't working correctly, so some debugging is in order there. Thanks for looking into this everyone.