It will have smart charging
First things first, check the battery, not just condition, but correct type. A lead acid battery will not work properly with smart charge, it must be Silver Calcium! Easy to over look.
Next, put a meter across the battery. Remember when you remove the smart charge 3 pin plug from the back of the alternator, it reverts to a conventional alternator! If you do not have about 13.8 volts, carry out basic charging system checks and suspect the alternator, its not a smart charge fault !
Correct charge voltage from the alternator, then its time to start on the smart charge system, and you will need a scope. First the system.
Pin 1 = Alternator Feedback
Pin 2 = Alternator Load Request
Pin 3 = Reference Voltage
Now, pin3, must MATCH battery voltage ! Its fed from a fuse in the CJB, and a high resistance on the fuse contacts causes a volt drop, and the smart charge drops out !
Next pin 1 & 2 need checking back to the PCM for resistance, isolation from ground and each other. If ok, its out with the scope.
Pin 2 is the request from the PCM to the alternator. This will be a square wave pattern that will change with load request. So lights, screens etc on and monitor for a change in the pattern. (Obviously back probing with the plug connected)
No change in the pattern means no request from the PCM, you should now suspect a PCM fault. Correct pattern and move on.
Pin 1 is the feedback from the alternator and MUST remain a constant square wave pattern. If this pattern mirrors the one on pin 2, the smart charge part of the alternator is faulty, and a new unit is required.