How to wire this new alt in?

I would get a test light and see how the new plug is wired. ie, figure out which pin on the plug goes to which place on the alternator. Then just translate it to the new harness.

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if you figure out the x goes to the wire that plugs into the center post, then on the new harness which ever one plugs into that place on the harness just make it go there too. If the old harness did not use the extra wire I dont know how the new one would either. The backs of those alts are the same so my first step would be to set it up without the extra wire and see what happens. Could always give the part place a call to verify.