I have the Ford wiring manual for '04. Orange with light blue stripe is the 'sense' or voltage reference wire. This goes to the battery junction block and gives the regulator the battery voltage to control charging.
The other one is not so simple - the light green/red wire goes to the PCM for 'alternator enable' and fault detection (lighting the 'charge' light). From the manual - 'PCM enables alternator by sending 8-9V to the regulator. There can be a delay to help the engine idle to stabilize after a cold start.' and 'If PCM senses 12V or 0V, it will send a signal to the instrument cluster to turn on the charge light.'
Probably your '03 is the same. But to do this right, you would need an alternator compatible with an '03 and not a 'generic' alternator that will bolt to a 4.6.