My personal experience (Running short tapered TORs) was that drilling the airbox and putting in a larger main jet (initially 130) resulted in a lean condition at partial throttle. You might try installing TBS or Thruxton needles to richen up the mid range throttle response. Right now I am running 125 mains and Thrux needles with the drilled airbox and short TOR's. The needle swap is relatively easy compared with changing out the jets, so don't be afraid to try it. Even putting a shim under the stock needle should help the symptoms described.
