Hello Terry
Are currently configured Services (running or not) set to use the domain you ultimately want?
If yes then you should be able to do this using the interface without any need to use the command line.
Before you try what follows (read it carefully first) I would make sure you have a fully working bootable clone of the server as it exists now. That way you could at least roll back to where you are now. Not perfect but you'll know that some things are at least working.
Remove the server entry in Server Admin and re-add it this time using its .local name (eg: server.local). If its already using this try its IP address instead or its loopback address. Once Server Admin has refreshed itself select the DNS Service and stop it. Delete whatever is there. Remove the Server's IP Address from the DNS Server's field in the Network Preferences Pane. Reinstate either the Router IP Address or your ISP DNS Server Addresses.
As an added precaution and only if the current domain (Kerberos Realm and Search Base) is as you want it to be Archive the LDAP Database. In addition export all your Users & Groups. If Users had Calendars prior to do any of this export their calendars from their iCal Clients. Save them locally for re-importing later on.
Quit out of Server Admin, launch and try to connect to it again. Hopefully you'll be able to do so. If its successful quit it again and now make sure the Server is fully up to date.
Once its fully up to date launch Server Admin and begin to build the DNS Service. You could use these instructions if you like:
http://discussions.apple.com/thread.jspa?threadID=1607034&start=0&tstart=0
For example you could use the relevant part that refers to DNS. It's your choice.
Once the DNS Service has been configured and started, remove whatever DNS Server IP addresses you placed in the Server's Network Preferences Pane and replace with the Server's own IP Address. You don't need anything else. Disable IPv6 whilst you're there.
Use the usual command line utilities to test and qualify the DNS Service. Once you're happy launch a web browser and see if you can connect to the internet. If that bit is working quit out of the browser and begin configuring your other services that rely on DNS. If you've clients that have been joined using the LDAPv3 plug-in remove the setting and re-do it. Make sure the edu.mit.Kerberos file is removed from /Library/Preferences.
Open Directory, SUS, iCal etc work best if the clients are using the Server to resolve their DNS. I would disable IPv6 on your clients as well. Ultimately you may still be looking at a rebuild anyway?
Hopefully this helps?
Tony
PS: I have tried the above successfully for 10.4 and 10.5 a few times and it has worked. The key is to be patient. Even when SA seems like its not responding stick with it.