Simple answer is yes, your stock harness will work. You will be modifying it some, but it will still be the stock harness. To get the stand-alone features setup, I would recommend sending the computer to lt1swap.com because he only charges $75 to get you to a start-up tune and beginning point. You will be able to start and run the vehicle, but it wont have a boost tune in it. That will be up to your tuning shop to get done for you, unless you know how to tune one and have bought HP Tuners software. The harness "trim down" is time consuming and a bit intimidating, but if you are comfortable with wiring you can do it in a day or two not rushing. Main thing to do first off is remove all of the plastic loom and pieces of tape holding it all together. Do that BEFORE taking a single wire out and you will be a lot happier when it comes time to remove wiring. I had never laid eyes on a GM harness other than what was under the hood of my 2000 Silverado and covered up from the factory and I did my harness in a day and a half, 8 aleve, and 9 large sweet tea's from McDonalds... The caffeine was a big help!! When I was done, I connected all my stuff up, and it fired off on the first turn of the key.
Something to note when testing your harness before starting: The fuel pump control wire will NOT activate an LED test light. It does not provide enough of a load. Try connecting the relay you are going to use when testing, it will activate that. If you hear it click on for 2 seconds, then off, you have it right!!
Don't let it scare you though, the harness job is easy when you take your time and double check your stuff before removing anything. Follow the guide on LT1swap.com and it will work perfectly. My harness came from an 01 Yukon 5.3 4x4, fyi.