Verify the following, on a FULLY CHARGED battery...
start the vehicle
test battery voltage while running.
13.7-14.2 VDC +- 0.1volts?
shut off car.. turn on headlights for 60 seconds.
battery voltage 12.0VDC or higher?
if the "running" voltage isn't enough, (like the same as the battery voltage) then check the "mega fuse". Its location can be found in the alternator how-to (duratec maintenance forum, in the "read first" thread.