Hi,Asuming you dont have all the pro tools (though you do have a code reader aparently) start with simple things.. check the cap, wires, and plug for Cyl 3 if everything looks fine keeps running till you see the light again and check the code. If its the same Cyl you could switch the plug to another cyl to see if the missfire moves. If it doesnt or you already have the tool then check compression. If its still doing it and everything else looks fine (which mine is doing) it could be the injector.
As for fuel... yeah, better be running something good. lol Also if it is bad fuel it would probably acure on more then one cyl.