Thanks for the help, I think I tracked it down ... It worked last night when I went to bed, but not this am ... Something had to change, and I kept trying to figure out what happened with the secondary domain / httpd.conf but I don't think that's where the problem was ... I think it is because I added the main server name to the DNS System as a server (go with the point if my terminology is off a bit) and put the IP Address of the secondary domain as the second IP Address. I just changed it ... It makes sense (to me anyway), because that would have populated after I went to bed ... Other than that, nothing should have changed.
I know the virtual host containers and permissions were (are) set up correctly, because when I use only the IP Addresses I end up in the right place ... If my permissions were off, I wouldn't have access, even by IP Address, and I wouldn't see the correct index.ext page for the given IP Address if the Virtual Host settings were incorrect, so it has to have something to do with the registration of server.example.com with the DNS System and the IP Address(es) I used, I think, for now anyway (lol).