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An alternator can run on two wires, the thick wire is the supply to charge the battery, direct to positive, via fuse box or starter supply. The thin wire possibly blue on Fords, is the energiser wire from the dash charge light, without this connected the alternator will not charge. If on the new pigtail two wires are thick (30amp) you can ignore one, some vehicles double up on the charge supply wire.
make sure the pigtail is plugged into the alternator and that the power wire is hooked to the pin on the back of the alternator, if there is no plug there you can get a replacement one from the parts house with a pigtail fairly cheap and just solder it in place