Would like to share a simple fix to a multi-hour search. Installed Multi Sites with sub-directories, all went well until I tried to access the added site or the original sites links. What I found on the WP Codex is that I must edit Virtual Host In Apache. Made the below changes bounced Apache and all is well. Hope this helps.
Joshua
<VirtualHost *:80>
ServerAdmin webmaster@localhost
ServerName http://boomurphy.no-ip.org
DocumentRoot /var/www/wordpress
<Directory /var/www/wordpress/>
Options Indexes FollowSymLinks MultiViews
AllowOverride Fileinfo Options <------------Change Here From"NONE" to
----------------------------------------------------"Fileinfo Options"
Order allow,deny
allow from all<--------This helps also
</Directory>
</VirtualHost>