Did your kit come with instructions? Are you sure you have the intercooler mounted corectly? I don't know anything about the IAP kit in particular but a few people on
www.ka-t.org would.
What do you mean "all the way through and over" ? Most people go through the battery tray and over to the throttle body if that is what you mean. Are you sure you have the right pipes? Cold/hot side not mixed up?