Use JuddiRMITransport.java. There was an issue with jUDDI's implementation of an RMI transport where it was ignoring the JNDI settings on a remote machine (https://issues.jboss.org/browse/JBESB-3071), which is why ESB contains its own version of an RMI transport for jUDDI.
I'm not sure whether that issue has been resolved or not, but I'll look into it and log a bug to fix the documentation issue you've raised here.
Other thing is that I've saw some /juddiv3 in configuration files*, but in juddi-service.sar there's juddi.war, in this case /juddi
in jboss-properties.xml there's:
<property name="org.jboss.soa.esb.registry.queryManagerURI" value="org.apache.juddi.v3.client.transport.wrapper.UDDIInquiryService#inquire"/>
and in documentation:
<property name="org.jboss.soa.esb.registry.queryManagerURI" value="org.apache.juddi.registry.local.InquiryService#inquire" />
Is this right ?