1.Defective spark plugs
2.Inadequate spark/coil,defective spark plug wire.
3.Lack of compression
4.False air leakage.
5.Faulty fuel injectors.
6.Insufficient fuel pressure.
8.EGR valve that is leaking.
10.Throttle position sensor.
11.Manifold absolute pressure sensor
12.Mass Airflow Sensor
13.Idle air control valve
Note: If it doesn't apply disregard it-
Monday, March 14th, 2011 AT 4:08 AM
Rasmataz is correct. However, the clunking sound worries me. This tells me that there are at least two problems. The first one is causing the rough idle(usually a vacuum leak, but now it can be almost anything). The second problem is causing the clunking. Without hearing it, but hearing you say it gets louder when you shift into neutral tells me it could be a bad rod bearing, push rod(could also cause rough idle) or flat cam lobe(also could cause rough idle).
Ruling out the vacuum leak is easy: Spray all vacuum connections and fittings with brake cleaner or carb and choke cleaner. The engine wills tumble badly when the leak source is sprayed. Also spray the interface between intake manifold and heads and carburetor (is so equipped). Unplug plug wires individually. The engine should smooth out a little if a bad cylinder is disconnected. Get the manual for your car and check to see what the voltage should be across the O2 sensor and tps sensor. Check the fuel pressure at the regulator. Check all of the spark plugs for carbon buildup or fouling.