Panels modules got rid of all my pages I recently installed a theme that called for Panels Everywhere, Mini Panels, and Page Manager modules to be installed.  The theme looks great but I don't understand where all my custom pages went?

I had created a bunch of pages in my custom module using hook_menu().  Now my site is completely driven by Panels and Page Manager.  I assume all my MENU_NORMAL_ITEMS were being stored in a block that is now being suppressed by panels everywhere.

How do I get all my old menu items to work with my new theme?  How do I link up the elements of my theme with my existing pages?
Panels everywhere is like it says, a way to use Panels all over your site. This means that whats normally outputted by page.tpl.php will now be run through a Panel.

Enable the site template (if not already done) here: /admin/structure/pages
Edit the site template and add the page elements as you want your site to be built. Eg. add the site header, then the page title, page content etc.

There is also a setting to create a sample site template variant for you here /admin/structure/panels/settings/everywhere.