Ok, I don’t think issue has anything to do with custom layouts or the theme; it looks like something is misconfigured with your WordPress installation and your permalinks.
If you look at your site, every page on your site is simply pulling the theme’s homepage file, as if it can’t find any of the pages on your site. I have a feeling there’s something screwed up with your Permalink settings. What happens if you go to Settings > Permalinks and put them back to “Default”? Do pages now show up properly?
If so, it means you’ll need to troubleshoot your WP install and how you’ve set things up. Here’s a lot of helpful information on this topics: http://codex.wordpress.org/Using_Permalinks