The simple answer is to just remove them, or tape the ends off and tie them back into whatever wire harness they come from. The other ends are at the regulator, which also gets eliminated in the conversion. If you really want to use the existing wiring, attach the "Armature" wire to the main charging terminal of the alternator and splice the ARM and BAT leads together at the regulator. The FLD wire at the regulator can be wired to the ignition switch or the idiot light ground, and the generator end of that wire can be used as the exciter lead at the alternator. I would reccomend running a new, heavier-gauge charging lead to the back of the ammeter, however, as the alternator output will be several times the capacity of the generator.
Jerry