Could you tell us how it runs at cruising speed? Any stumbling? What about when you're accelerating quickly, does it stumble or miss? The reason I ask is that the video shows the stumble taking place when the throttle comes to an idle which would indicate the stepper motor isn't picking the idle up quickly. The stepper motor is out of the circuit off idle. If acceleration and cruising appears normal, I'd check the stepper motor and reconfirm the primary TPS was adjusted correctly. The stepper motor can hang up a bit if things get a bit dirty. This is usually corrected by spraying penetrating fluid under the rubber boot on the motor. You might want to check for a vacuum leak also. This usually affects the idle circuit more than anything. No problems with cruising and full throttle pretty well point to the idle circuit and vacuum leak issue. Also, check to see if the primary wire connectors (2 per coil) are tight. These do come loose causing a miss at times.
As to your 2nd dealer blaming the RamAir then removing it, (and I assume converting back to original) I wouldn't go back. Obviously their mechanic has no experience.