Q: Engine running rough and light now on.

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Engine initially started running rough on up hill acceleration (felt like ruts in road), then engine light came on (code tested manually crank x3 with no error), and now running rough in flat conditions. Vehicle purchased 2 mths ago from dealership who was to have inspected for resale/replaced alternator. EGR valve had been replaced in April, and after purchase on trip through hilly conditions engine light/EGR code came up again and found quite dirty so cleaned it [tests okay now] as well as sticky throttle body which dealer replaced. On purchase new champion plugs replaced with iridium ones and fuel injector cleaner added. Now on noted problem 90 Octane gas tried and just put in a fuel cleaner. Orig owner parked vehicle every winter (6 months) in garage and suspect fuel stabilizer was not used re EGR/throttle body issues. Initially was suspecting plugged fuel filter but questionable after reading symptoms on line (no start problems as yet). Possibilities/things to test?

My car has 65000 miles.

Yes you could have bad fuel in the system if that is the case. However, you may want to check and make sure your fuel filter is good, and make sure there are no extra leaks in the the air intake. Too much air will cause a problem with running. A local expert from YourMechanic can diagnose the rough running issue and Check Engine Light so that this can be corrected properly.

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