Hanging a Jace on the wall is our backup plan if this gets to complicated or painful.
It might get complicated if you are not able get a hold of LN-Builder or something similar. You would have to weigh cost ratios. It might be cheaper to get LN-Builder and do the integration directly. I don't deal much with JACEs, but I know that LN-Builder is around $500. Though Johnson should have given the database and software over during initial install. Unless it was done through a service contract.
If you happen to have the Workbench Pro tool you could use that to commission the LON equipment, instead of using the LN builder. I don't know how the NAE gets setup, but the subnet and node of the Trane equipment I have set with the Tridium tools. I did find it a PIA to sort out which set of data (SCC or DAC) was the proper set. Of course that was my first exposure to LON.