Mine got a steady Check Engine Light two days after the engine was replaced. It came back with random misfire codes for various cylinders. The dealer tech had to do a 'crankshaft position relearn' process and that cured it.
PS - I don't like your 'idling rough' comment because that was the first symptom of my piston letting go. After about five miles of rough idling, the CEL came on steady, then the next morning it began flashing. The piston on cylinder 8 had cracked the top ring land. Hope yours is something else.
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