[LS short box]

I haven't bought any LS swap harnesses on Face book. On my LS swaps I've used Speartech and Howell with good success. I buy the ECM/TCM from one source so if there is an issue I have one supplier to talk to. They also supply a base tune so it will run once you get that far. I would suggest a chassis tune to really dial it in.
The alt charging cable should run from the main lug on the starter over to the main lug on the starter. None of the harnesses that I've ever used had that cable integrated in to LS swap harness. I typically run a 6 gauge cable from the starter lug to the alt lug. The swap harness should supply a single wire to the plug on the back of the alt.
The 2006 engine could be a a 24 tooth or 58 tooth crank reluctor wheel. You to confirm before ordering a harness. 24 tooth cranks need one ECM for engine and trans. The 58 tooth cranks needs an ECM for engine control and a TCM for 4L60E control. Crank tooth count also makes a difference in regards to the TCC/brake light operation.
Are going to run the 205 TC? Does the speedo cable run off the 205 TC? Do they make a 4L60E to 205 adapter? If you are using the 4L60E it will have a port for the VSS signal.
And you can't have enough good grounds. Battery to engine. Engine to frame.
Good luck with your project.