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Using info in http://drupal.org/node/1674192 I was able to put together a custom plug-in, but am having some issues debugging some of the error messages that are popping up.
After uploading the new plugin files to /custom_layout/panels/ and flushing the cache I get the following error:
Notice: Array to string conversion in at_get_plugins() (line 38 of mysite.com\sites\all\themes\adaptivetheme\at_core\inc\plugins.inc)
When I go to change the panel layout, I get the following errors (and also the page will not load panels at all)
Warning: include(mysite.com/sites/all/themes/mysubtheme/custom_layout/panels/three-15-60-25.tpl.php): failed to open stream: No such file or directory in theme_render_template() (line 1495 of mysite.com\includes\theme.inc).
Warning: include(): Failed opening 'mysite.com/sites/all/themes/mysubtheme/custom_layout/panels/three-15-60-25.tpl.php' for inclusion (include_path='.;D:/UniServer/usr/local/php/includes;D:/UniServer/home/us_pear/PEAR') in theme_render_template() (line 1495 of mysite.com\includes\theme.inc).
I've also attached the plugin files if anyone can have a look over them. Any help would be greatly appreciated.