Go back and look at the alternator diagram. There is a resistor and a indicator lamp in series with the switched 12 volts. You are seeing the voltage drop across them, which is to be expected. Anytime you pass current through a device, be it a resistor, lamp, solenoid, motor, coil or whatever, there will be voltage drop across that device. It's known as Ohms Law.I'm leaning towards the battery charger thing as misleading. I typically will charge the battery while not connected to the car resetting the computer. Since ditching the charger theory/idea the battery is 12.+v every morning.
Key One Engine Off: I checked the LtG/R wire at the alternator and got 12.8v but when plugged in it was 3.8v?
I'll start drop voltage testing tomorrow. With the way the computer/car can run great then not that seem to coincide with the low oil and possibly the coolant dash lights, the slight buzz in the stereo, there's more to this but in a nutshell this really feels like some type of short.
It's fun to mess around with the Stang from time to time but this is starting to take it's toll. Countless hours and very few cruises this season, well, sucks.
Thanks everyone for your help.
If you did see a full 12 volts, with the green wire plugged in, it would be a cause for concern.