After about 10 hours with this I finally have everything back to running again.
Since I see more than 30 people read this without reply, I have an idea that maybe someone else has seen this issue too so here is what I found.
1. Deciding to do server maintenance, more than one thing at a time can cause yourself issues
like doing a yum update and working on an ssl certificate too.
2. The initial problem of NamedVirtualHost has been my own fault from the beginning. There is no need to add your server IP address in the list of available IP addresses, this causes two entries in your /etc/httpd/conf/vhosts/Vhosts_ispconfig.conf file. Removing the duplicate solved the NamedVirtualHost warning.
3. I also noticed that named was not running and then realized with some reading here that the permissions on bind had changed with the yum update and was causing that problem. Following one of Falko's post I reset the permissions and dns came back up.
4. httpd would still not restart but now it was just "failed" and not mentioning the NamedVirtualHost warning or error. A check of the error log yielded NOTHING. A config check of httpd.conf passed as ok and this was driving me crazy. What I learned off list is that the ssl module in Apache is worthless for giving any errors in the log files. So my next step was to look at my ssl section of all my virtual hosts in /etc/httpd/conf/vhosts/Vhosts_ispconfig.conf There I noticed my directive for my bundled godaddy certificate I installed had the wrong web id on it.
So what I really learned is LOG files help, but when it comes to http not starting and nothing is gleaned from the error log..... LOOK at all your ssl statements in your virtual hosts config file because it appears very little to nothing will be logged from ssl statement failures and httpd will fail to start without showing any errors!
I hope this helps out other new guys to Linux like me!