mdkd16y7e

Alright I have a 1999 Civic LX with the stock D16Y7 engine. It has been rough idling, idles around 500-700 when parked. When I brake it goes down to about 200-300 rpms. The engine has a lot of hesitation/vibration too, there are no check engine lights, it seems to have slow pick when accelerating on the highway and the gas mileage has been bad. I have replaced spark plugs, spark plug wires, distributor, ignition coil, TPS sensor, cleaned the IACV, and replaced the throttle body gasket. Also the timing belt was replaced recently along with the camshaft positioning sensor. It has a short ram air intake on it to. I want some input on what might be causing this? Anyone have any idea's?