Sorry to hear man! A rod knock shouldn't be caused by a CAI unless it caused a really lean condition. VTC has nothing to do with it either neither does the catch can.
As long as you're not tuned you should be fine so think positively!
Also, see this thread for advice if GM wants to pin the mods against you
http://www.camaro6.com/forums/showthread.php?t=471953
Keep us posted