When I go to Tools-Network I get a message box that states the following: "Warning: An existing WordPress network was detected." I assumed that this warning had something to do with my SuperAdmin not showing up.
Okay. On mine I get this:
"Notice: The Network feature is already enabled. The original configuration steps are shown here for reference."
That means you didn't set it up correctly somehow.
I have modified the .htaccess and wp-config.php as I was told in the article on WP codex.
Undo that. We'll start over, basically :)
1) Add THIS to your wp-config.php
define('WP_ALLOW_MULTISITE', true);
2) Go to Tools -> Network
That should bring you to a screen that says something like this:
http://twitpic.com/1tunbn
Basically, what you've done is set it up out of sequence. I'll talk to Andrea, who wrote that page, and see if we can't get it cleaned up for RC1 :) She wrote that WAY back before Beta, when we were all still on Nightly.