Yep, have the carbs balanced and have the idle mixtures set the rich side of smooth running. Most bike mechanics don't know how to tune idle screws, so it may be a problem for you.
 These engines are known for having a stutter or miss at around those rpms, it's the camshafts causing reversion in the intake ports.
 Even after playing with all that, I still have a slight stutter, mainly on neutral throttle, say going through a corner, but it clears immediately any load is put onto the engine.
I don't mind it, it doesn't hurt anything and it gives the bike character, reminds us of it's Ninja heritage!

 Regards, Andrew.

 Vstrom is gone, on the hunt for a GTR.