Oh definitely no neg effects. I just did that this weekend. Basically, the egr system is located on the right hand side, under the cowl. All you have to do, is cut the pipes going to you manifolds, and then crimp down the pipes to seal the manifolds. Then, you can unclip the egr system, unplug if from the AIR system (this is done the right hand side, its the tube that runs over the wheel well), and then, pull out the little vacuum tubes that go into a little cylinoid (some of the tubing goes to the rear-left of your intake, and is a BITCH to get undone) There are some other vacuum tubes back there, leave those, and then you'll have to plug the hole with a screw, which is what I did. You will also have to leave the cylinoid plugged in so you won't throw a SES light. Then remove the rest of the vacuum hoses, and pull that **** out. I think i'm going to remove the AIR system this weekend during my free time. Should drop like 20lbs hahaha, that **** is heavy appariently. Good luck to you!!
Regards,
Adrian
BTW, I have a LS6 intake I could sell to ya if you're interested. I just took it off this weekend (put a 90 FAST on), and its in perfect condition. You'll have to reuse your port seals, and this one comes with the seal for the throttlebody. I also have brakets, and bolts ect.... Send me a PM if you're interested.