I left most of my original wires in. Oil pressure, temperature, volts, A/C, speedometer and tach wires were all left and reused. Sensors were also reused with adapters to fit the LS block. Speedo and tach wires were fed directly to the new PCM. I left in the old PCM and wires and mounted my new PCM under the hood on the driver's side. I'm going on my 3rd year with 20,000+ miles without any incidents or problems.

Lots of research is needed as stated above. Brendan Patton's site was extremely helpful and he also flashed my PCM. I used the original harness and modified it to stand alone as Brendan indicated. It took about 2 months to complete but was well worth it.