Something went wrong with the installation and setup. I deactivated the plugin (network) and restored the config.php statement that had been commented out for the plugin.
Looking through the forum, I saw that you advised to restore the wp_blogs table and wp_[blog ID]_options table for affected blogs. I changed the wp_blogs table but can not figure what needs to be changed in the wp_[blog ID]_options table.
Right now I can see all of the sites in the network: Good but I am getting 404 errors going to the sub directory sites