2002 Ford Escape

My wife got stranded in her car because it would not shift into gear, the auto windows would not work, the dash instruments would not work and the headlights would go out after 30 seconds and come back on for a short time only if you turned them off and back on. After doing a little research I determined it was the alternator because I only have 11.5 volts at the battery when the car was running. I checked all the fuses and they were good. I installed the new alternator after having the store check to make sure it was good. I still have the same problem. I was told to check the voltage on the small yellow wire at the alternator to see if the voltage was the same as at the battery and it was. I also installed a new battery. What would you check next? Thanks Steve