You really should have kept that alternator. What you have now is a huge unknown that may last years, or a week.I got a new alternator and the voltage stayed the same. Maybe just a little over 12. But I unhooked the smarty and put it to the stock settings and the dead pedal is gone. Everything is right now exept the voltage is still low. It should be right at or under 14 shouldn't it
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.