I know this is a couple of months old, but there are a few companies that can help you out. Of course there is Painless Wiring (800-423-9696) and there is another company that I am going to use. They can take your original harness, and rework it to a stand alone one for $320-$360. (so they say) They can also flash your computer to suit your needs and transmission combo, or provide you one. They are
www.wait4meperformance.com My buddy has used them to do the same combo in his 83 C-10 with a 5.3L and I'm impressed with the price. I'll be going with a Gen III 6.0L (LQ4) and a 4L65E trans in my burb.