Every so often after a cold soak? Consider it could be something as simple as evaporative purge cycle running.
The PCM schedules an EVAP purge at a random time after a cold soak. Expect some rough running depending on how much gas vapor is in the charcoal canister.
OR... there could be a vacuum leak in the EVAP system. This causing excessive air during the purge.
Do you have an ODB2 scanner? If so, monitor when the PCM switches from open loop to closed loop. Does the rough running happen before or after the switch?
Next monitor the EVAP purge PID (it may be called canister purge). Does it relate to the rough running?
OR... is it possible there is to much worrying going on?
OBTW, clean the MAF.
Try this old racer's trick. Run the car in a totally dark location. Look for the blue light which is evidence of arching.
Any smoke from the exhaust when it is first started? If so, what color?
Another possibility is oil leaking down the valve stems. It pools on the intake valves. It runs rough until the oil is burned off.
