Update: Found the problem, talked to the experts at MAD Electric. They helped me out and told me the cables I'm using were to small to carry the current. I'm using like 2gauge and they said no smaller than a 1/0gauge. After the car is started and run for a while obviously everything heats up. With the smaller cables they cannot carry the current under the heat, the amps and the volts go down. Anyway these guys are the best, if you every need any help with battery relocate or any Ford wiring, please contact them.
www.madelectrical.com Thanks Vortex for the help!

Check out there article in the Oct. 02 issue of 5.0.
