First, about building your own "full stack" of Chef Server.
Opscode is going to release a full stack package of everything required for the Open Source Chef Server soon. This was demonstrated at ChefConf last week, and is under active development for a near term release.
The demo was in a keynote talk by Chris Brown and Adam Jacob. The demo starts here, but the entire thing is interesting, giving a look at the upcoming features for Chef in 2012.
The new omnibus build system for Chef consists of a couple repositories. First is the build system itself. Then, the repository for building open source software commonly used. Finally, the repository containing the build instructions for Chef itself, including both client and server. You're welcome to check these out and give it a go. If you need further help with them, the Chef developers mailing list or #chef-hacking channel on irc.freenode.net are the best resources.
Next, about managing configuration.
Since you're using Chef, you should manage the configuration with Chef itself. The demonstration (and the built packages from the omnibus projects above) uses Chef Solo for configuring the server, though it can be a chef-client to itself too. How you approach that is up to you, but store your Chef configuration in a source code repository, whether that is git or another system.