I am a new 2006 XB12X Ulysses owner and have been busy reading this forum, searching for modifications and doing some of them. It had a K&N filter so I thought I would use a rotary hole saw to open up the top of the air box a bit. Drilled 3 holes in it and noticed that there was a better growl at about 3000 rpm with no noticeable power improvement. What I didn't notice at the time and connect it to the air box mod it that that the holes made a lifter like tapping noise/lifter/cam noise when the bike warmed up. I guess the holes where letting the injector noise or other mechanical noise be heard more. So I taped the holes up with masking tape and the noise went away.
So, the lesson is that if you want a more quieter bike, do not modify the air box.