I'm 99% sure the '06 carbs are the same as 01-05.
The stock size pilot jet is 15.
Traditionally people would get 17.5 pilots, but I hear that Mikuni isn't making them anymore, so they may be tough to find. There is no problem going with a 20.0 pilot. (Some people even get 27.5's)
But if you haven't already, before you replace the pilots I would make sure that...
1. The carbs are in sync.
and
2. You have tried to tune out the roughness with the A/F screws.