Cel Help Needed

[griftsense]

OK here it goes...
I've owned my a4 1.8t for 6 months. Within 2 weeks of ownership cel popped on with a cylinder misfire on cyl 3 and 1 I believe, perhaps it was a multiple and a cyl 3 misfire. At any rate, spark plugs were replaced and for the next 5 or so months (7kish miles) the problem appeared to be fixed. However within the last couple of weeks the cel has come on (never flashing) with codes of
random cyl misfire
secondary airflow
cyl 3 misfire

I should also mention there are no symptoms or loss of power when this happens. the car drives fine. the only oddities are at idle there is a 1sec "cough" or very slight flutter when warm(has done this before the spark plugs were replaced). Also if the car has been sitting over a cold night or for a couple days on startup it flutters 5 or 6 times before catching its "breath" then all is fine(noticed this happen after the plugs were replaced).
mechanic checked spark plugs again as well as wires hoses etc, all fine.
I have the updated coil pack (j i believe)

lastly, the most recent 3x the cel light has come on when its been about 1 mile from my house (when i leave) and at btwn 2k-2.5k rpms.

Since I doubt the dealership will replace anything unless the car starts bucking or not driving normally I was hoping to gain some insight on my problems from the astute users of this form. any help is greatly appreciated.
I've been told to shorten the gap on the spark plugs but what does that do with secondary airflow as well as the cel popping on. any suggestions? thanks