I'm guessing you are too rich, not too lean. Sounds like you also might need to syncronize your carbs. See Dinqua's instructions:

Go here and click on Syncronizing the carbs

At that link you will also find good instructions on rejetting.

Another good link that I use when I rejet is at Factory Pro

Your air mix screws might not be set the same. They should be close to the same. Also with bigger pilots you don't need as many turns on your air mix screws. Turn them out counter-clockwise to richen, in to make leaner. To get a proper adjustment you should turn them all the way in, carefully, not tight, just so you feel them hit bottom, and then turn them out about 2.25 turns to start with. Run your bike until it's good and warm. Turn them out 1/4 turn each and see if that increases the idle. Blip the throttle. There should be little or no hesitation. Turn them out another quarter turn (richer). Keep doing that. Once your idle tops out then back them off (turn them in clockwise) a quarter turn. With the jets you are running you shouldn't be out more than 3 - 3.5 turns. I'm guessing you should be at 2.75 - 3 turns. Take a ride. See how that works. You may need to adjust from there. I find that I need to adjust my air mix screws after any modifications like rejetting. I'll go for a ride, stopping occasionally to turn them in or out to see if feels and sounds better. I might do that 3 or 4 or 5 times until it feels right. I try to adjust both the same, a quarter or an eighth turn, and then ride and test.

My point in messing with the air mix screws is to get them even and the same. Same point with syncronizing the carbs. If you have one black plug then something is out of balance. The air mix screws only affect the throttle just off idle, and has a minimal affect on high throttle.

You don't say if you are running stock exhaust and airbox. Unless you have removed your snorkles and have less restrictive aftermarket pipes, I'm guessing your jets are too rich. I run 45 pilots and 138 mains. I tried 140s and found them to be a little too rich. I have my snorkles out and I run Staintune pipes, which are a straight through pipe with no baffles. They are pretty unrestricted. I've tried a number of jet combinations and I'm starting to acquire quite a collection.

Another thought. You could pull your air filter and top cap that holds the filter in place. That should let it breath better. Fire her up and see if that makes a difference. If it does then you are definitely too rich.

Here's my disclaimer, this is an art, not a science. There are a lot of unknown variables here, pipes, air box and filter, altitude, state of carb syncronization, humidity. And there probably are others here who would completely disagree with my methods. I'm only telling you what has worked for me.

Hope this helps some. Good luck.
John

I was born a long ways from where I was supposed to be. - Bob Dylan