Uuuuh.. that line you left unhooked should be plugged, eh. It's a vaccuum line for the intake runner if I remember right. That leads to a resevoir with a solenoid on it.. you're supposed to disconnect that and then cap the vaccuum at the intake manifold. I don't have a AEM intake but if you didn't to that you could get unpredictable results. There's a page someplace on the net detailing the install.
My bad for not reading your post through
.
Steve
EDIT: I knew I wasn't crazy.
http://www.lightningmotorsports.com/...ai_install.htm
That should get you on the right track.