I'd leave the 2nd throttle plates alone unless you have a ton of money for dyno time to realize what is probably a small gain if any. Back when ECU Editor came out a guy by the name of Petrik, who developed it, did lots of testing. He said the factory setting on the plates at 94% made the most power, any more open than that he stated it lost power probably due to turbulence in the TB If you chose to pay with them let us know the results I'd be curious.
I have that STP map set by Smith in my saved Gen2 Busa unrestricted bin file.
It does make a difference.