While all I have done to my bike so far was to install the Gunships from Tailgunners, without the baffles, TTS Master Tuner, and kept the stock Ventalator with the K&N filter... when my Mech did a quick flash to compensate for the increased air flow, it started to misfire at 2,200rpm at cruise when the outside temperatures were approaching 80 degrees, and occasionally stalled when at idle.
He found quickly, that the tune he used was incorrect, as he thought I had baffles in the Gunships. I'm only 1 of 2 people in Alaska that are running the Gunships, and the other set are down somewhere around Anchorage. So, he had never seen them before.
He put it on his dyno, and found out also, that the Idle Throttle Position was reading 5.5 instead of zero. He asked me the strangest question... "how do I shut the bike down after the ride"? I replied mostly at the ignition switch, but sometimes when I'm rolling into the lot for a group ride, I'll shut it down at the Run/Stop switch and coast in.
He said that the electronics in the throttle position, was a learning system... meaning that any input on the throttle while the bike is being shut down is being learned that that is the zero position. And, tuning it properly with the throttle position at any value other than zero when at idle, is a gamble. Making the numbers work is almost impossible.
I noticed a thread on here recently discussing how to reset the Idle Position. Without any input on the throttle, fire it up, let it run about 20-30 seconds and shut it down at the ignition switch. Repeat this 5 or 6 times and the Position Sensor should be learning the new zero postion.
We did this while connected to the dyno and watched the changes as they happened.
While we didn't get the position back to zero, we did get it down to 4.0.
He then pushed a map for the Ventalator with 'Racing' exhaust, and all of the hesitation/misfire/stalling went away... even in somewhat warm weather.
He said that any of us with the electronic throttle systems should never shut down using the Run/Stop switch, as there is a risk that the throttle position may not be neutral when we do so.
He recommends that we shut it down with our right hand at the ignition switch, so that there's no chance of any input on the throttle postion.
I hope this helps, and that my lesson saves you some diagnostic time.