I find your first post confusing. Let's try to clear it up.

The voltage coming from the alternator is low when the AFC is hooked up. What voltage does it put out?

The voltage goes back to normal, around 14 volts, when the AFC is disconnected.

Ok, what are the settings on your AFC? The only connections I can see are wiring problems with the AFC shorting something or a similar problem, or the correction on the AFC making the car die out and idle too low.

What is it idling at when the voltage is too low? Have you set your idle properly recently?