I went ahead and created a folder to make all of my work in so that I could zip it up later or have the Rsync server grab it and save it in the main infrastructure.
This will generate the randomized string create the csr.
openssl genrsa -out domain_name.key 1024
This will create the CSR for GoDaddy which will you will need to copy and paste into their site. If you are going to be requesting a Wild Card SSL make sure that the NAME is *.domain_name.com
openssl req -new -key domain_name.key -out domain_name.csr
Now log into the GoDaddy site and paste the contents from the above CSR into their site. When you get the email back I suggest putting the 2 files they give you in the same location as you created the above. You will most likely have the following files.
With those files you will need to setup the SSL virtual host like the below:
<VirtualHost *:443> ServerName subdomain.domain_name.com ServerAdmin firstname.lastname@example.org DocumentRoot "/home/user/vhosts/site_down" DirectoryIndex index.html index.php ErrorLog /var/log/apache2/secure_domain_name_error.log <IfModule mod_ssl.c> SSLEngine On SSLCertificateFile "/home/user/csr/_.domain_name.com.crt" SSLCertificateKeyFile "/home/user/csr/domain_name.com.key" SSLCertificateChainFile "/home/user/csr/gd_bundle.crt" </IfModule> .. The rest of your config file </VirtualHost>
From here you should have no problems with the GoDaddy certificate. Hope this helps everyone.