I never changed fuel map after removing them and loved the difference it made.
I think that your bike may be suffering from being too lean on low end now that there is just too much air.
The secondary throttle plates are not there to optimize performance, they are there to limit and not to increase.
Do you know why the Gen 1 had no STP´s? Because it had an ignition timing retarder on the first gears to emulate the STP effect - it could be easily tweaked by a device that fooled the gear position sensor, the famous TRE. It does not work on Gen II Busas.
I think we all can come to the following conclusion, after Brad´s report:
More air flow from down low means the POSSIBILITY for more power to be made - however if it results in a lean or rich mixture, it will result in less performance.
Kind like a situation where one introduces forced induction with high pressure, but the stock injectors cannot cope with so much fuel needs and the end result is unoptimal power because of a too poor mixture.
With that said, I am surprised Brad did not report that even with less power, the throttle response (resolution in low rpm) difference is amazing. I still think that the throttle response difference alone is worth the mod, even if it made slightly less power (not the case with mine, guessing mine did not result being lean on low rpms after STP removal).
I agree, the performance of my bike isn't bad by any stretch, I can just tell it does need more fuel. But according to my sparkplugs, it's not too lean either.
So you're still running the stock fuel map? You do have ECU Editor too right?
You should try changing the stp settings and see how much it improves, and then let us know!