I am mainly creating this issue to act as a point of reference for the next person that needs to do this.

Due to JRA-13529 we need to upgrade the Jira Soap Client

I upgraded the client using the maven 2 instructions here: http://confluence.atlassian.com/display/DISC/Autogenerating+Jira+SOAP+Client+Classes+Using+Maven+2
Using the wsdl from JIRA 3.12.3-#302

And I had to add a method to the JiraSoapServiceServiceLocator class because the url of the jira instance the wsdl is from is hard coded into the client

 public JiraSoapServiceServiceLocator(String address)
    {
        this.JirasoapserviceV2_address = address + "/rpc/soap/jirasoapservice-v2";
    }