You will not use the original alternator harness.
Your fusible links need to go to the battery.
You should be using the positive cable from the 6.0L, with a fuseible link for the alternator output jumper to the battery cable.
I kept the purple crank wire for the starter.
I used the old switched ignition wire as the Hot during crank and run for the ecm.
I kept anything running to a guage sensor. I kept the wiper and fuel sender wires.
I kept the A/C wiring.
I kept the cruise harness, with added wires and mods under the dash.
I moved the battery to the driver side with a tray from LMC.
I built my own main power bus: from the positive terminal of the battery, the big cable goes to the starter, and picks up the alternator at the power lug. The crank wire is routed from the booster, to the motor, down the left side of the intake, where it joins the battery cable at the power lug next to the alternator. Both run down and cross nunder the motor to reach the starter.
The smaller positive cable jumps, from the battery, to a master fuse (175A). The same size wire jumps to a power buss with several lugs. Both are on the core support beside the battery. The fusible links from my electric fan relays, ecm and fuel relays, and the firewall harness are attached to these lugs. Fuses protect the relays.
The negative battery cable is connected to the block. Heavy ground wires run between battery and frame, block and frame, core support and frame (both sides), block and firewall, fuel tank and body, transmission and frame, and two from the bed to the frame. Your efi harness should have two ground wires that go to the back of the cylinder heads.
That help?
