The migration tool doesn't find any content types due to this, so I can't run the app and have to remove the configuration manually I guess. What do I have to remove from the EPiServerFramework.config, only the SiteGlobalFiles, SiteDocuments and SitePageFiles? The Modules still need to be there I suppose.
Hav you added any media types to the site? An empty VPP should not affect this, but if you don't want to migrate anything just remove the VPP's you mentioned.