Wow ... didn't know they made a 6g, yet. What happened to 4g and 5g alts?
Try typing in "alternator swap" in the search and see if that yields more results. There's still a ton of topics lingering around here with pics and all, and JRichker always has a slew of diagrams and such on hand that help out a lot.
As far as the wires, it depends on the plug to which you're referring. The smaller D-shaped plug doesn't get clipped at all, it just plugs right into the 3g alternator as-is; the fat, flat plug only gets the black/white wire snipped, whereupon you crimp/solder a little spade connector on there and just poke it right into the other connection on the back. Just leave the plug with the other two orange wires hanging there out of the way, and don't disconnect them at the other end on the starter solenoid, as they still do serve a function elsewhere in the car.