Thanks for your post, it helped get a little further. However if you have any ideas on the following I would be most grateful:

I cannot restart those services using /sbin/service/ * start and they are not running
I also have no /var/clearos/samba/initialization directory, only /var/clearos/samba/lock

These issues I believe are preventing me from going forward. In my GUI I see Samba prompting me to initialize but when I hit that button I get to the old config and cannot start the service again and cannot change any details of the domain or server config

Would really appreciate any pointers

FIXED!

I had to reinitalize the directory services

from http://www.clearcenter.com/support/documentation/clearos_guides/trouble_initializing_directory

Perform the following steps to re-instantiate the directory initialization routine:

 rm -fv /var/clearos/accounts/initialized 

rm -fv /var/clearos/accounts/config 

rm -fv /var/clearos/ldap/initialized

rm -fv /var/clearos/openldap/config.php 

rm -fv /var/clearos/openldap/status

rm -fv /var/clearos/mode/mode.conf

rm -fv /var/clearos/samba/init* 

/sbin/service smb stop

/sbin/service nmb stop

/sbin/service winbind stop

/sbin/service nscd stop

/sbin/service nslcd stop

/sbin/service slapd stop

FYI this did fix the original issue, but broke authentication on everything else, such as samba and my domain. Samba gave me the initalizing error which runs indefinietly. Was able to fix it with the following.

From http://www.clearfoundation.com/component/option,com_kunena/Itemid,232/catid,18/func,view/id,39747/

1. check the system log file which said "SAMBA is already initializing".

2. check to see if the smb, nmb and winbind services were running and found that they were not.

3. found a lock file in /var/clearos/samba/initialization that appeared to be preventing the system from starting the services. 

4. deleted the lock file, went back to the Windows Networking GUI and clicked initialize again. That got me to the next screen which prompted me for the host and windows domain names.

5. I changed the host and windows domain names and the the system is humming right along now

The only thing I wasn't able to fix was the domain. Nothing I could figure out would allow my computers to rejoin the domain. I kept getting an error where during joining from windows 7 it was saying that it could not find the domain via dns.