The wiring of the 3-g alternator is very simple for the mustang. The hardest part of the conversion is the clearancing of the aluminum bracket which isn't too bad - just some grinding in a few spots.
As for the wiring. The d shape (3 wires) connector is plug and play from old alt to 3G. there is a small white single connector right by the d connector you need to take that wire and splice it into the white wire coming off the d shape connector. The main two charge wires you just unplug from the old alternator and tape up securely in the harness - they should not be used but are needed because they do connect some wiring. just tape them up where the contacts won't ground and leave them alone.
Then you need minimum of 8-9 gauge wire to go from the charge terminal to a recommended 150 amp fuse and then to battery.
I used this fuse and holder for mine:
http://cgi.ebay.com/ebaymotors/ws/e...0503968857&viewitem=&sspagename=STRK:MEWAX:IT
Basically I bought this and two battery cables with the ring terminals connected the back of the alternator to the fuse on one side and the other side fuse to the battery positive. seen some hook it to the relay where the battery positive goes too. I mounted the fuse on the drivers side shock tower.
Nice thing is that I tapped my stereo feed from this fuse termial.