with old alternator i got code 41 with new one on i got 47
41 would point to bad alternator or worn brushes
47 means that although the field voltage varies from the PCM there is no voltage variation on the battery (12v+ feed to the PCM) so that can mean either a bad ground or bad connection on the charge wire coming from the alternator. I would take the Jeep to the store you bought the alternator from if the ground and connection is good as it could be something internal. doesn't sound like it's the PCM since it was detected an open circuit before and now has a different code (if it was the same it could have been the PCM).
You could also measure the voltage right at the alternator to see if it's higher than at the battery, that can clarify if it ground or "+" cable.