You have a timing issue, it's either your cam, crank, or timing belt. I had a similar issue after recent major internal engine changes. HP Tuners has a complete write-up on this issue in their forums.
According to HP Tuners, the ECM/PCM retains timing data based on your prior engine specs and any major changes to the engine/drive train will trigger this DTC and symptom.
You must do a CRANK RELEARN so that your ECM/PCM captures the recent changes in your engine/drive train. Otherwise, you run the risk of internal engine damage.
According to HP Tuners, most shops, and even dealers are UNAWARE that they must do this. The Chevy dealer that did major engine work on my SS DID NOT do this and my car was consistently misfiring and throwing DTCs.
Ford Mustangs have the same issue.
I did a CRANK RELEARN and no more issues and the car is smooth as a baby's behind!
http://https://www.youtube.com/watch?v=XELjn3z3GgE