Here's the correct way to do the 3G wiring. Follow this, save money and it will be done the right way.
Stangnet 3G install sticky
http://www.stangnet.com/mustang-forums/646825-3g-alternator-install-how.html#post6673702
The old wiring harness contains one yellow/white wire that is the voltage sense wire. It purpose is to measure the voltage drop between the alternator output and the body wiring buss. It will cause the alternator to increase its output voltage if there is a significant drop between the alternator output terminal and the body wiring buss.
That wire must be present for the alternator to work. For that reason, leave it in place when using a 94-95 Mustang 3G alternator. If your alternator is not a direct one for one swap with a 94-95 Mustang 3G alternator, that may not apply.
Here's the wiring diagram to show why...
Do not connect the black orange wires to the alternator: tape them up out of the way. Here is the reasoning behind using only a single 4 gauge fused power feed to the alternator. If you use the two 10 gauge black/orange wires in addition to the 4 gauge wire, you have two fused power feed paths. The total current capacity of the wiring is the sum of the fused paths. The 4 gauge path is fused for 125 amps, and the two 10 gages wires are fused for 60 amps. That is a total of 185 amps, which exceeds the capacity of the alternator. Overload can occur without the fuses blowing, damaging the alternator.
The worst case scenario is that the alternator develops an internal short to ground resulting in a catastrophic failure. The initial short circuit surge current is limited by the resistance of the wiring. The current in a parallel circuit divides up according to the resistance of the branches. If the 4 gauge fuse opens up first, the two 10 gauge black/orange wires will be carrying the short circuit surge current. Depending on the time lag of the fuse links, they may open up before a fire starts or they may not.