I would stay away from the one-wire. See other posts regarding one-wire vs 3-wire alternators, specifically a link posted by Alan Horvath. I suspect one of your unused wires is for the field connection to "energize" the regulator/alternator and likely part of the alternator light circuit. It is possible that the other one was connected to the output, or possibly a "sensor" wire. Is your existing harness in good shape? If not, you may want to re-wire from scratch, then you get to customize your harness for all the stuff you are going to use and where you are going to use it. I think a nicely wired truck adds greatly to its functionality and appearance; I have seen some real "rats nests" at car shows. Lots of nice chrome but the wiring looks like crap.
