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I am sorry to hear about your engine performance issue you are having. I have soon good news as this diagnoses will not be that involved.
That is correct. This check engine light is strictly for emission purposes only. It can come on with or without a performance issue. In your case, the engine is running rough causing the emissions coming out of the tail pipe to go higher than normal. This is why the light is on.
However, lets take this one step further. The computer flashes this check engine light when the computer recognizes a catalytic converter
damaging misfire occur while the engine is running. It does this to alert the driver as a precaution not to drive the vehicle very far. If so, the catalytic converter can be overheated which can shorten the life of the converter so it is recommended not to drive the vehicle if the check engine light is flashing.
So you are going to want to get the engine performance issue fixed as this will stop the engine from running rough and the check engine light will no longer flash. In fact, once this is diagnosed and fixed, you can get the computer cleared and the check engine light will no longer even be on.
You are going to want to start by checking for diagnostic trouble codes in the computer. You can pay a tech to do this or you can do this yourself if you get your hands on a code reader or a pocket scanner. A lot of times your local parts store will even do this for free for you. Once you know the code in the computer, you can go after the root cause.
My experience has been that this will cause misfire codes in the computer (because the engine is misfiring). From there you can go after which cylinder is misfiring and fix or replace the root cause of the misfire. Usually when we see this in the shop it is just bad tune up parts but it would be a good idea to check engine compression and fuel delivery (on that cylinder that is misfiring) just to be sure there is nothing else going on.
The cost will depend on what is bad and the shops labor rate you bring your vehicle to unless you decide to do the work yourself. In that case, it would just be the price of the part or parts that are needed. Usually this is not an expensive repair especially if this is just bad tune up parts causing this rough running condition.
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