You only posted part of the error so I can't really tell what is causing it.
To produce a minimal build you must start with a clean checkout of the code from the source code repository and only open, compile, and publish the mojoportal-core.sln. If you ever compiled the main mojoportal.sln solution then the post build events of the other features already copied all of their files into the main web project so there is no way to get a clean copy without them at that point.
Hope that helps,
Joe