You can dissect the harness fairly easy. You just need to know what plugs/connectors need to stay in the harness to make sure your motor wont throw a code after you re-tune the ECM. Your tuner will need to know all the details, so they can tune accordingly. A wiring diagram will show every pin number and color on the ECM. Just remove one by one untill your done. Re-loom the harnes, plug it all back together and your done. I have done this one time with my last build. I had a 2000 LS1 that I put into a full tube chassis, custom offroad truck. I had the mail order tune done by "Wait 4 Me Performance" in Texas for $75.00 a couple of years ago. Go for it, and good luck!!
...........Workin' on it...........