I thought about posting this on the Windstar area, but since it is a smart charge issue it should not matter what area I posted in. I have a 2003 Windstar that has been having an on going issue with the Batt light coming on or off or just staying on. The Alt is sending 13.8 volts to the battery, but this is lower than the 14.0 volts or higher that the PCM wants to see. This post may get a little long and have a lot of information. I have been working on this for some time and I am the type of troubleshooter that does not like to throw parts at something and hope for the best, I want to know the root cause of the failure. The following are the readings I am getting with a voltmeter.

Key Off

Battery Voltage 12.6 volts
Connector off the Alt, these are the connector readings.
Pin 3: 12.7 volts
Pin 2: 0.0 volts
Pin 1: 0.0 volts

Alt pin readings
Pin 3: 0.0 volts
Pin 2: 12.6 volts
Pin 1: 0.0 volts

Key on Engine Off. The Connector is off the Alt.
Connector
Pin 1: 8.8 volts
Pin 2: 0.0 volts
Pin 3: 12.6 volts

Connector on Alt and back probing.
Pin 1: 0.0 volts
Pin 2: 0.8 volts
Pin 3: 12.6 volts

Engine Running No Load
Battery: 13.8 volts
Pin 1: 0.5 volts
Pin 2: 7.0 volts
Pin 3: 13.8 volts

Engine running and electrically loaded
Battery: 13.1 volts
Pin 1: .4 volts
Pin 2: 6.5 volts
Pin 3: 12.9 volts (the voltage of the battery was going down the longer I kept the full electrical load on the system)

When I revved up the engine to 2000rpms the voltage to the battery came up to 13.8 volts. Removing the electrical load from the system and at idle the battery voltage came back up to 13.8 volts.
Now for some unknown reason after the load was removed the battery light went out and the following are the readings I observed.

Unloaded
Battery: 14.1 volts
Pin 1: 3.7 to 3.8 volts
Pin 2: 0.1 volt and the highest was 1.7 volts. This is the signal from the PCM every five seconds.
Pin 3: 14.0 to 14.1 volts.

Loaded
Battery: 12.2 volts
Pin 1: 8.7 volts
Pin 2: .1 volts
Pin 3: 12.2 volts

With it magically kind of working again after a heavy electrical load on the system I am thinking may be the alternator has a bad connection in it that is making contact when the alternator is hot. This could also explain why when I pull the three pin plug off the alternator when the engine is running the voltage drops off drastically on the battery. I have read that the alternator should go to basically a limp home mode of 13.8 volts when it is not getting a signal from the PCM,

The battery is not a silver calcium style battery, but there is a lot of controversy over whether a standard lead acid battery will work.

I anyone has any input that would be great, if not at least there is some troubleshooting info for others that may run into this in the future.