The manual says to replace the air filter every 8000 miles. I would suspect the same caveat applies as with other applications, "more often in dusty conditions..." I have found that my bike runs better if I pull the air filter (stock) and blow it out everytime I change oil, (4000 miles) and replace it every second time (8000 miles).
I use the Carbtune everytime I do this and the synch is always off somewhat. I also use it every time I make any mod that may affect performance.
I don't know if the adjustment is being affected by vibration, but there is always a minor adjustment to be made and a noticeable improvement afterwards.....