If spkwindgdn1.spkaa.com is the target hostname of the system, then that command looks correct except for the the username. The username and password you should use in this command are the credentials for your WindchillDS admin user. The username is usually 'cn=Manager'.
Though, the error that you're getting when running the script is a NoClassDefFoundError, which is probably an issue with your environment rather than the command you're using.Make sure you're running the command from a Windchill shell. If you unset the ANT_ARGS variable before running the command, then try opening a new Windchill shell and running the script without unsetting ANT_ARGS.
For the repository, you're right that there aren't any more changes needed there. Since your LDAP entry doesn't include the hostname, and since the domain hasn't changed, the current entry will work with the new hostname without needing any changes.