All Confused HELP!!!

OK, Here are some photos. First question. This is the stock harness from M&H. Because I am going to run a direct 8 or 10 ga wire from the alternator to the positive battery post on the starter relay (or should I go directly to the positive battery post?) should I just cut and dead end the positive wire on this original harness. I believe the other two wires go to the alternator fields for the voltage regulator, correct?

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