When I did my swap, I yanked the entire harness... But I wanted to rewire everything because i'm anal. You can leave it in and just use the GM harness for engine function. You really don't need to modify anything (GM got it right), just get HPTuners and remove VATS. Going with a T56 makes things even easier since you don't have to deal with the harness for an automatic. Also, use a drive-by-cable throttle body to make things easier (LS2's came with both drive by wire and drive by cable).
Also, take note that GTO T56's are slightly different than FBody T56's. Both work, but will take a little modification depending on which one you get.