Hi there,
1) You can set extra classes in the assets, to remove top/bottom padding/margins. Check the advanced section of the page builder documentation – http://dante.swiftideas.net/documentation/#swift-page-builder
2) This is answered above.
3) Please make sure you have the latest version of Dante, and the logo width/height set in the theme options.
4) Ensure all your images are optimized (try the smush.it plugin) and you have Better WordPress Minify and possibly a caching plugin enabled.
5) The shop appears in 3 columns with a single sidebar setup, and 4 columns with no sidebar.
6) Have you checked this guide – http://support.swiftideas.net/knowledgebase/replicating-the-demo-naked-header-example/ ?
Hope that helps!
– Ed