Guys, please bear with my ignorance.

I am getting close to starting wiring the nova and I am getting a little nervous. This is my first ground up build and pretty much my first wiring job besides stereos and other basic items. I am very comfortable with running wires cleanly, making good connections and soldering. But not familiar wiring a complete car. I've done tons of research and have purchased an American auto wire update kit, and a psi harness. I will be running 2002 ls1/t56, vintage air, dual electric fans, electric fuel pump from tanks inc, and Dakota digital dash. I am concerned with blending the harnesses. To start, What in the AAW engine harness will be required for the ls swap and what can be removed? I know there will be more questions about relay and such at a later date. Thank you for your time.
Here's a screen shot of the diagram for reference.
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