Hey cool beans, speartech is a good place to start for aftermarket harness. Also a google search will help you out a lot.
For my setup, I'm using MAP sensors, with my ITB's. Also for a standalone ECU I'm running HPtuners. If you're wanting the most out of that supercharger, I highly recommend a Standalone or at the very very least a ECU Flash.
Stock vs. Aftermarket depends on what HP you're looking for. 6.0 LQ9's IIRC Heads are liked because the drop the Compression Ratio which allows you to add more boost. Or you can go into patriots heads etc. etc. Intake on the cheap, find an LS6 maniforld, intake on the expensive Harrop ITB's or FAST induction systems. Again its really all of a matter of what your goals are that determine where you go aftermarket and where you stay stock.
Check out these books from amazon, or go down to your local Barnes and Noble or Borders and look at the LS1 performance rebuilding stuff. I haven't ran across a horrible book yet. Most will be able to get you started in the right direction. Also check out http://www.ls1tech.com and just read around.
http://www.amazon.com/s/ref=nb_ss_b_0_5?url=search-alias%3Dstripbooks&field-keywords=ls1+performance&x=0&y=0&sprefix=LS1+p
Hope this helps,