Engine missing on highway

[pulsar2121]

I have a 2012 Yaris with the 1.5L and 5 speed manual transmission. I bought the car new in November of 2012 and have accumulated 21,000 miles over the last 14 months. I have had no problems with the car before now. Well, except for the crappy single windshield wiper setup, but I'd consider that a design flaw.

Recently the car has been having 30 to 60 second periods of misfiring while going down the road at highway speed. The check engine light flashes and then goes away when the issue stops. The other 99% of the time it runs perfectly fine. I can usually count on it to happen a couple of times a week. I hooked my OBD2 scan tool up to the car and got a misfire code for cylinder #2 and nothing else. The next day I took it to the dealership where I bought the car since I am nearing the end of my 25,000 mile warranty and had them look it over. Needless to say, they weren't able to find a problem with the vehicle.

For a little history on the car. About 11 months ago I had the muffler removed and replaced with a piece a straight pipe. You know... for fun! Also, about 5 months ago I had the gas nozzle from the station pump get stuck in the car. It took turning the nozzle upside down and pulling hard to remove it. About a week later I noticed that the little metal flap in the fuel pipe going to the tank was missing. I really doubt that either of these two things would be causing the issue, but you never know. Again, I haven't had problems with the car up until a few weeks ago. Any suggestion would be greatly appreciated as our average temperature outside right now is around 0 degrees Fahrenheit and I don't feel like walking when this car dies on me.

[Exiwolfman]

pull the plug on 2 ....maybe all and compare also see if anything up also with coil...odd possibility bad fuel....