Engine hesitation

I just had a new engine put in and have had the car back about four days. Today, I noticed that the car was hesitating while at a stoplight but became more pronounced as I continued to drive. By the time I arrived home, it was hesitating during acceleration and driving but almost not at all while in park. The check engine light also came on, but it was late so there was not a place to take it to where I could check what code it was throwing. My guess, because the engine was just installed, is the timing. But would the timing cause the check engine light to come on? Anyway, I am extremely upset because I waited two and half months to get my car back and it is the only one I have. The mechanic who did the work did it as a favor and I do not want to take it back to him because every time I have I seem to have a bigger problem than the original. I know the best thing to do is to take it to the nearest auto parts store in the morning, but I wanted to know if someone had an idea of what the problem is?