Unplugging the battery is a commonly-mentioned step. It supposedly clears some adaptation or fuel trim tables the ECU maintains, making the bike "re-learn" the new system faster. Don't know if there's authoritative technical basis for that, but owners report it often helps. It's easy to do and hurts nothing.
The K1200S O2 sensor is narrow-band only -- just a small range right around stoichiometric, or 14.7:1 air/fuel ratio. It also only functions at very light throttle, under about 15%. IOW it's useless for air/fuel tuning under many conditions, esp performance-related scenarios. It operates "open loop" (without O2 sensor feedback) much of the time. The bike will actually run fine with the O2 sensor disconnected completely -- no check lights, no "limp home" mode as with some cars.
How and IF the KS measures increased air flow from breathing mods and injects more fuel, I don't know. There is no Mass Air Flow sensor, as on a car. Rather the KS uses a more basic system called "Alpha-n", simply a lookup table with throttle angle on one axis (Alpha), and engine speed on the other axis (n). E.g, at 50 deg. throttle angle and 4500 rpm, use x injector pulse width.
It biases the output of that up or down based on environmental conditions such as ambient temp, coolant temp, barometric pressure, etc. That way if it's 0F, 100F, you're in Flagstaff, AZ (7,000 ft), or the bike is cold starting, the mixture stays more balanced for those situations.
However it does NOT measure mass air flow, nor even manifold pressure. Without these there is no way (I know of) to even approximate air mass flow via measurement, hence no way to trim air/fuel based on breathing improvements.
My '06 KS was dyno'd with air/fuel probe before and after the EVO intake and Akropovic exhaust. Peak power increased from 140 to 149.5 rear wheel hp, and the air/fuel ratio stayed safe. It's slightly lean at a few points, but it's in the safe range and won't burn a valve or anything. I could pick up a few more hp with some air/fuel tuning, but that requires the Dimsport Rapidbike3 system: http://www.technoresearch.com/Produc...Rapid-Bike.htm
There are also wide-band O2 systems that continuously provide real-time feedback over the entire engine operating range. Ironically some are available for Harleys, just not our fancy German bikes: http://www.daytona-sensors.com/tech_wego.html
So besides the overnight battery disconnect, there's nothing you can do. The KS engine management apparently doesn't know about the breathing mods, but evidently there's enough conservatism built into the air/fuel map so the EVO intake and Akro exhaust is safe.