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Q: cold rough idle and P0303 code , run great after clearing code and warming up,

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Did timing chain job, new coil pack wires and plugs, clean up valve and new valve cover gasket, new exhaust manifold gasket, new IAC sensor, new tps, new fuel injector to cylinder 3, new air filter, oil change and filter change, new crank shaft sensor, new cam shaft sensor.

My car has 200000 miles.
My car has an automatic transmission.

Code P0303 suggests a misfire in cylinder #3. This can happen for many reasons such as a vacuum leak, weak fuel pump (pressure), bad ignition coil, low voltage to the fuel injectors (causing pulse problems) or a faulty mass air flow sensor, all of which can cause an imbalance in the air/fuel charge in that cylinder. Try checking to see if you are able to replicate the misfire and see if it happens more under load or at idle or if it is completely just intermittent. This may help to narrow down what types of components to check.

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