You really should have kept that alternator. What you have now is a huge unknown that may last years, or a week.
If you disconnected the batteries when changing the alternator out you changed the APPS calibration. It is possible you have a dead spot in the APPS, but I wouldn't worry about that until you get your charging issue rectified.
In the future just pull the codes with your smarty and look them up on the web making sure it is Cummins specific.