Tim: The more I learn about what you've got the more I doubt I can help you. But I do think your answers to my questions will help others following this who have relevant experience and can jump in. So one more question...
Do you have all the NCE equipment installed and connected to JMRI and is it all working? If not, is that what you'd like help with? Or are you looking for help in setting up the back and forth scripts?
Jan
