What is the output of the alternator with the battery disconnected? If you start out with a charged battery and can start the motor how long will it run? Will it run if you start it then disconnect the battery? What is the no load voltage on the battery charged then what is the voltage reconnected? Just because you have a new battery doesn't mean it is any good. I've run into a couple bad new ones over the years. You may have a short somewhere. Is the battery heating up?

Is it the factory wiring? Carbed/injected... what did you cut out of the wiring, because there's internal and external regulated alts.... Year make/model original engine?

Its the original 4.6 motor, we ran the first week no problem and all the sudden we have this problem.  We didn't change anything.  The car will only stay @ 12.5 even when running.  We can run 10-12 laps before the volts drop to 8 than no throttle response at all.  We swapped to a fully charged battery out of another car, same reaction.  The one thing we did is run some new gauges but we left the original wires connected.  Its really embarrassing I heard a fan say we suck.  Sorry its @ 95 w the reg attached to alt

Sounds like the electrical system is overloaded. Do you have an amp meter in the car? There must be a short somewhere with enough resistance so you don't blow a circut. The alternator is probably only putting out 8 volts all the time and the 12 volts is the battery voltage. Either that or the voltage regulator is shot. Take the alternator and battery to a shop or crappy tire or parts source and have them tested. I know they are new but until you can absolutly rule those two components out then you will be chasing ghosts all over the place. I am also pretty sure that the computers in those cars signal the electrical system for charge rates so the computer may be done.