[shorod]

There is a trimmer screw on the ambient light sensor/amplifier to adjust at what level the lights attempt to turn on. There is a chance that this potentiometer is dirty and causing the flickering, but I would be more suspect of a bad solder joint (not all that common with Ford electronics) or a grounding issue. If I'm interpreting what you typed correctly, if you turn the headlights on manually with the switch, they no longer flicker, therefore the problem is not going to be with the wiring for the headlight bulbs directly.

The light sensor/amplifier on your 1999 Taurus is located in the right hand (passenger) side of the instrument cluster near the windshield.

-Rod