Curious. Did you get the "Japanese spec" because of the VIN#? The firmware version won't matter as long as the tune matches if you change it. Different firmware versions actually store the fuel map in different places in the memory. Although ECMDroid (and later versions of ECMSpy) won't allow you to download the wrong firmware version map, TunerPro will and that will definitely cause you problems.
I would not recommend changing or tweaking the ECM until you diagnose the bike much further. Tweaking the ECM now would just cover up the problem.
I don't believe just adding a K&N filter would cause the ECM to enrichen the entire fuel map almost 30%! But leaking intake seals would. O2 sensor maybe, clogged fuel filter or injectors, weak fuel pump, anything restricting fuel flow. The basics really. Theres no way to diagnose this over the web, anyone guessing is just guessing. You'll have to get dirty. Post up what you find!