Oh man, the answer was staring me in the face the whole time. I just realized tonight after looking through some of the mydnsconfig files that the actual php files that load up on the net for mydns are stored in /var/www/html/mydnsconfig by default. When I added the virtual hosts, httpd stopped looking in this directory because I keep the domains in /var/www/"example" hence mydnsconfig would not start up. Now what I did, is move the mydnsconfig directory to where one of my domains is and now I just have to type "mydnsconfig" after the domain name and BAM, it works.
I also created a virtual host in httpd.conf for my name server and I pointed it to the default mydnsconfig directory. So now it can only be accessed if someone types my IP or ns1.example.com before mydnsconfig. So there are different approaches to the situation.
Here is a short virtual host example:
ServerName ns1.example.com/mydnsconfig // I added the mydnsconfig after ns1.example.com so if people still type just ns1.example.com it will redirect to man domain I want to load up. //
CustomLog logs/ns1_access_log common
ServerAlias example.com *.example.com
CustomLog logs/example_access_log common
Now I just need to setup the connection for mydns to use ssl and I'll be good to go!
This may not be important to you, but I wanted to let you know that because of the alphabetized way programs startup when fedora boots, mydns tries to startup before mysql and this leads to some problems. I fixed this though.
What I did is:
When you enable this service at any run level it creates links in /etc/rc.d/rcN.d/ ("N" is the runlevel number)
called S98cups and K10cups
All of the SnnXXXX files are executed in alphabetical order at startup.
All the KxxXXXX files are executed in alpha-order at shutdown.
2 digit nums are the rule, and generally the Snum and Knum sum to about 100 unless you have a reason otherwise.
Talk about hacking the configuration for the service startup order.
So I did: ls /etc/rc.d/rc5.d to view the contents of run level 5. I noticed S52mydns and an S64mysqld in the directory. Now this is a problem because mydns has a lower number so it boots before mysql.
I also noticed there were some open values between S64 and S70. So I created a file S68mydns and I put the contents the S52mydns into S68mydns. Besides this, S52mydns had: # chkconfig: 345 52 50 inside the file but I changed it to 68. Even though it is commented out, I thought I would update for consistency. I did a reboot and it worked; mydns started after mysql.
Here is the link to the thread on it in case you want to find out more on how I fixed this:
Thanks again for everything and all the great information you and your team are putting fourth on the internet.