My 3.2 manual ran perfectly fine with a 2.6 ecu and the inlet, injectors and throttle body are identical. Similarly, that ecu was used for diagnostic purposes in at least two other cars without issue.
Your initial query almost four years ago was to replace the 2.6 with a 3.0. No mention was made re gearbox, but the suggestion was made to swap the 2.6 sensors and harness onto it, but that fitting a 3.2 made more sense as everything was guaranteed to fit.
Two years ago, you were adamant that you wanted to fit a 3.2 ecu. Again you were told that it wasn't necessary. Yet here we are...
TB has explained how the 2.6 ecu can be 'corrected'. It already contains the map required. Yet you tried to have the 3.2 ecu programmed.
The issues stem from the drip feeding of information. For example:
Are you still running lpg?
How is it running the 3.2 ecu if you haven't changed the transponder?
It’s possible that the details are getting lost in translation