EGR and emissions etc are hooked up, I just noticed that when the FPR vacuum hose is off the car idles a lot smoother, yes vacuum hose is plugged off. i am running a stock airbox, i was using a dry flow filter but the differences arent much (only noise differs). Everything is hooked up, no misrouted hoses or wires, but the idle is still rough for the first 15 mins of driving