Well, it can have many causes. Since it comes and goes, I don't think it's a permanent mechanical damage (by the way, do you still have the first timing belt? then I would change it soon despite the low mileage of the engine).
So I would assume an electronic fault or a loose contact of all the electrical plugs or cables, starting with the MAF sensor plug. Do you have an OBD2 reader? That helps because some errors are stored directly. Unfortunately not all. As you describe it maybe a malfunction of the hydraulic timing of the camshafts? I had with my Sigma 1.6 4/4 a problem with the contact of an injector, that also led to the rough engine running. It was directly visible in the OBD2, even which of the 4 injectors it was.
