Create a hidden menu (i.e. a menu that should not be displayed to site visitors) from the Menu Manager and add articles as menu items. You do not need to create a module for this menu, since you are not going to display them in the external interface. When creating a menu item, Joomla tracks aliases and displays them correctly.
In the sidebar, you have friendly search queries ... so you renamed htaccess.txt to .htaccess? Also check this out.
If you are having problems with specific links giving 404, check all your menus and find duplicate aliases.
Please also see this topic: http://forum.joomla.org/viewtopic.php?p=1896103
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