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!