If you look around at some of the older posts, you'll find that this has been a common problem. I bought mine with 2miles on odometer and by the time I had 500 on it , it was running just like yours. I sychronized the carbs, which helps a bit but doesn't get rid of it entirely. Time is the other thing that helps, seems to improve with mileage.
A couple of months ago I opened up the exhaust which leaned out the carbs even more than factory. Yesterday I changed the slow(or idle) jets from a #42 to a #45 and shimmed the needles with a #4 washer. Before I did this there was some hesitation and surging. 70-75 mph would make the bike seem like it was straining. Now with the carbs done, I have no hesitation, sputtering, or surging and it pulls hard through all gears. Smooth, just the way it should be. The carb work is easy to do, had the whole thing done in less than two hours.
Hope this helps. I'm sure somebody probably has other remedies that would also help.

Psycho