Q: Engine running rough and light now on.

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.