Intermittent engine misfiring

So my vehicle listed above started acting up. When I drove to work a few days ago about 30 miles away my car was fine. But on the way back there was this flapping noise at idle and while driving. When I accelerated my car would start to kick and shake, but when I accelerated quickly it didn’t do it. The check engine light was also flashing. When I got home the codes said it was engine misfire in the second and sixth cylinder. I changed the spark plugs and that didn’t fix it. So I changed the ignition coil and I thought it was fixed, drove fine all around town. When I drove to work it was great but when I drove home the problem came back. I shut the car off and turned it back on, it was a very hard start. It was also idling really rough and almost stalled out. I turned the car back on and kept going and the problem went away. I also noticed that when I start my car and I hear the flapping the problem will come back, but I can shut my car off and start it again and the noise usually goes away. Any ideas what it could be? Please help.