Option 3: LS1 builds, you have the most fun ahead of you! Not only do you need to re-work the stock driveline harness to stand-alone, but you will also need a new 12 circuit body harness!
If you are looking for detailed information on LS1 pin-outs, harnesses, etc. the site for you is LT1swap.com No one has a more detailed instruction manual for these. You can also send your PCM to him for programming. He does an outstanding job.
Be prepared for tedious work. An LS1 harness takes me about 15 hours to re-work.
I hide all the wires under the intake to keep the motor looking as clean as possible.