It sure would be handy if there were schematics that showed what original wires to delete and what original wires to keep in an LS swap when using a purchased harness.
Starting on wiring my 72' Chevelle and using PSI harness but trying to decide what original wires can be eliminated.

 

Take a look at www.lt1swaps.com , he has a pretty accurate wiring pinout to follow depending upon the PCM you are using.

 

in the same boat at the moment. lt1swap.com didnt really pinpoint what we're looking for, at all really.

 

Pm me your email and I can send you the info,

 

What 'original' wires are you talking about? I'm going to assume you mean the wires in the Chevelle since you bought an engine harness? Depends on your set up, but you can usually get rid of the alternator wiring since it will be controlled by the PCM now. Other than that, maybe some gauge wires can go, but the starter wire you need to keep, and the power wire for the coil will need to power up the ignition relay in the LS harness, so there really isn't that many wires left.

 

I ripped out every single original wire in the car and replaced it with the body harness, engine harness and fuse boxes that came from the engine donor car.

 

I think I understand your question now. Like ls171nova says, you can eliminate right back to the bulkhead plug the alternator, oil pressure, temp sender and possibly a couple of others. I also went to the inside and removed the unnecessary wires from the dash wiring. If you google the wiring diagram for your car you should be able to get a pretty good diagram.
Make sure to leave the main switch wire like he said as well. You can use that to activate the rest of the LS electronics. Once you get going the picture will develop, it really is not that hard to do.