I just tested the shaper on one of my test servers, and everything installed as expected; after the install process, I did all the recommended updates, and the problem you are having appeared. One of the recent updates to Image and Content Fader required changing some filenames for the plugin; this means that when WP updated the plugin, it couldn't find the old file, so it deactivated the plugin. All you need to do is go to the "Appearance->Plugins" page in the admin and re-activate Image and Content Fader, and the layout will return to being correct.
Most of the images are contained in widget content (Appearance->Widgets), but there are also some background images that can be re-defined in the theme options (Shape 5 Theme).
Adding "?tp=3" to the end of any URL on your site will show you exactly which widget position each widget is located in (
Example), which should hopefully speed up the process of customizing your site.
I hope that helps!