Mcbassin start with this page and as you scroll down and he color codes what should be kept and what should/can be removed.
http://www.lt1swap.com/2000harness.htm
Also on that page you can click on the year of the harness and it shows what each PCM pin does/where it goes to.
Here is another way he shows color coded what needs to stay and what needs to go
http://www.lt1swap.com/2004vortec_pcm.htm