OK, making some progress here. I added a brand new subdomain, in which I can now see the tools, domain mapping menu option. The other 5 subdomains I have were single wordpress installs that I moved into multisite. I have not deleted those single installs, as Hostgator noted I should leave them alone unless there is a space issue later. I believe these 5 subdomains are mapped correctly, as I have can see the correct mapping in the network/all sites screen. I guess all is working ok. My only concern is the 5 installs, what will happen if I delete those single installs.
