Thanks for reporting these issues.
The web.config problems are due to a current NuGet limitation on how it does transforms, so you will see duplicates in the ideablade.configuration section if it was already present, as well as the serviceHostingEnvironment element. In all cases you can keep your existing config elements and remove the added content.
We hope to get the web.config problems, and the problems with additional files such as global.asax and DevForce.cf, fixed in the next DF2012 release.