You are right about the "/store/?cat=5" problem. I'm not sure why wordpress is not showing up properly. I've contacted the module designer for WOZ module for help. Do you have any idea on how to make sure the URL comes out: "index.php?main_page=index&" instead of just "?"?
For the Module Manager problem, I figured that out. When I uninstalled SSU the first couple of times, I thought that admin/includes/module_installation and admin/includes/templates were only SSU files and I deleted the whole section. Forgot that MM had files in there too.
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