You have a aftermarket reman 2G alternator. They were prone to fires. The fire started at the two slip on black/orange wires that run side by side and are the output wires for the original alternator. They got rid of the slip on connections, and now you have to cut both of your black/orange wires (they are larger than the other alternator wires) and they should have supplied yellow butt connectors with the alternator. The two black wires coming from the alternator get butt spliced to the two black/orange factory truck wires in the harness. It doesn't matter which one connects to which, the two black and the two truck black/orange wires are the same, they just used two for current capacity reasons.
Your white wire beside the black wires loops over to the other small plug correct? The other small plug should have a yellow which goes to the truck yellow, white which loops to the white, and a green which goes to the truck lightgreen/red truck wire.