If a 6.7L Controller was replaced, navigate to "Misc. Functions" and perform all applicable routines:

WARNING: This page is about a different car, the 2011 RAM Pickup. However, it is still accessible from the selected car via links, so may be relevant.

NOTE:

The available routines may vary depending on model and year of vehicle.

PCM/ECM Replaced - Located within the Security Module
Injector Quantity Adjustment
Enable / Disable Vehicle Features - need to enable features
Set max vehicle speed
Set max cruise speed
Idle shutdown timer
PTO RPM adjustment
Set PTO Max vehicle speed
NOTE:
The numbers can be retrieved from the old PCM/ECM using the scan tool if the PCM/ECM is still functional or they may be retrieved from the Fuel Injectors themselves. The numbers are stamped on the intake manifold side of the injectors.
Reset Regenerative Filter Timers