The factory plug to the regulator will plug right into the 3g alternator. The other rectangular plug will have two black/orange wires going to it which will not be used (these are hot wires so make sure they are not exposed.), and a smaller wire I forgot what color that will need to be used. You just put a small female connector on the wire and it will plug into the stator plug which is the small male prong coming out the side of the 3g. You will also need to run a 2ga or bigger power wire from the starter solenoid to the alternator, and should upgrade the size of your engine ground wire to at least 2ga. You have to install a high amp inline fuse on the power wire as well, it'll need to be at least 125amp fuse. They don't really sell a "harness", if you do buy a wiring kit it will be extremely over priced.
I dont know why I typed that all out, there are sticky's with diagrams on how to do this. I must be too bored.