So I'm experimenting with uSiteBuilder (from Vega IT) to bring some of my sites up to a more enterprise level. I did release the tool "Umbraco Masterpage CodeFile Fixer" in early 2012 and updated it with uSiteBuilder support recently. In some of my experiments I got the error "No node exists with id '0'".
Quite simple for me since I build and deploy a separate binary with all uSiteBuilder stuff. Remove the binary from the bin folder and run the install process by navigation to http://yoursite/install/. This will setup or fix the root node. When done, you may try to place the uSiteBuilder binary in place again. Cheers.