DMN is correct - all settings must be reviewed from scratch. With the Mathis/Technoresearch tools there's a "reset TPS" procedure that must be performed if the ECU is changed. The TPS is not loosened and rotated like the "old" Ducati's, now the TPS is simply reset to a zero point via the software interface. The throttle bodies and then especially the airbleeds MUST be dialed in for proper airflow/CO balance (TB's set for cracked throttle airflow, airbleeds for idle airflow and CO balance). Then, CO level (mixture) must be set at the right level (4-6% I believe for idle CO). Then proper CO balance at Idle needs to be checked again at idle. The factory tools (tubes) attached to each header are invaluable for this procedure. If you're simply inserting a CO meter into the tailpipe, the CO balance attributed to each each cylinder will be difficult to discern.
Another thing to consider with a idle/dying issue is the automatic idle control found on the newer Ducati's. The device could be sticking or not functioning at an optimum level (quick enough response) which could cause the motor to stall. Again, the Mathis/Technoresearch tools have diagnostic capabilities where they can test the IAC (Idle Air Control). They can also view/clear diagnostic codes recorded by the ECU. But, the stalling could be as simple as bad fuel or a bad connection somewhere - even on a new bike. May want to check belt tension/cam timing (with proper cam lock and crank lock tools when adjusting belt tension) and check valve clearences.
I'd focus on setting up the ECU and throttle bodies correctly - don't waste time with the Powercommander - especially if it doesn't allow for raising the rev limit or if it doesn't allow for revising the ignition timing. Usually a Ducati Performance ECU will revise both the rev limit and ignition timing (more aggressive) - you can't beat all the development time devoted to the DP ECU compared to only a couple hours on a dyno with a powercommander. Also, what the Powercommander tuner might not tell you is that if you DO reset the TPS, throttle bodies, airbleeds etc the Powercommander will need to be remapped as the mapping created for the unit is only for how the bike is set up at that moment! Same goes if adjusting belts, doing a valve adjust etc. That's one of the reasons racers have their Powercommander maps checked/adjusted at each track - not only to suite the local environment, but also to optimise for any engine maintenance/upgrades between races.
