New ECU is in, not sure if I was doing something wrong but took 4 attempts to get it to actually sync as detailed above. Not sure if it made any difference, but entered the EKA using Nanocom on the last try.
Suspect the battery is a bit flat which may not have been helping either. But its now running on all cylinders again. Now to just properly fix the wiring which was bypassed to eliminate the gas ecu from being the problem.