Hmmm okay, I wasn't 100% familiar with your bike's mechanics, but I think you have hit the nail on the head - sounds like you need to lift the secondary needle up a notch or two (I raised mine using small washers, has the same effect). From the sounds of things you still have your original carbs handy? Have a look at those and see if the jetting / needles are any different...
Just remember, once you drill something out, you can't go back!
1990 CBR250RR - fully rebuilt and awesome!
1999 CBR900RR - a work in progress...
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