2006 Saturn Ion Jerks when shifting

I have a 2006 Saturn Ion 4 dr sedan with a 2.4 L. I have just recently replaced the air filter, coincidence or not, and had my engine light come on. In the same trip in my car I began experiencing jerky shifting. On my way home I decided to stop by Autozone to have then read my codes. Unfortunately my wife discaded the paper with the code analysis. It was associated with the timing. She continued driving the car for a couple days and the engine light was no longer on. I continue to have a shift problem. It shifts hard when shifting into a foward gear from neutral or park. It also shifts hard under most any degree of acceleration. I looked over the mounts and see no obvious issues.