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I ran across this same problem on my 98 trooper. Everything was fine for years, then one day out of town the battery was dead, or nearly dead. Got a jump start from someone and I checked the voltage and was only getting about 12.2 volts from the alternator.
Got I home and put in a new alternator and still only getting 12.2 volts. After much testing and prodding, I determined that the gain control in the PCM was not working. Unable to determine why it was not working, I ended up disconnecting the wire coming from the gain control circuit. I now get 14.2 volt charge from my alternator and everything is fine.
Not the proper way to fix the problem but it works for me.
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