Removing Air
Couple things, do you plan on installing a ls6 intake minus the egr setup? If you are going to do headers and remove EGR/AIR system you might as well...if not you have to get a block off plate for your intake. You will obviously throw a code when you remove EGR/AIR but it won't effect performance. If you have someone with LS1 Edit that can help you, you can delete them from your system so no code. But as far as removing it is simply a matter of unbolting and removing, nothing special.
Good Luck

