Rough Idle Following Head Gasket Replacement

Just replaced the head gasket on my daughters 2012. When I put it back together, I discovered it had went out of time by one tooth on the crank shaft sprocket so I took off the timing chain cover and reset that. All the mark line up the way they are suppose to, so that appears to be good now. Went to start it up and after the initial rough idle it smoothed right out then back to rough idle again and then will smooth out again. There is no check engine light and therefore no codes.

Did not replace the sparkplug or ignition coils at this time. They were all replaced recently. A the the head gasket was going, these could be my issue if they were affected by moisture.

Any ideas?