This might just have been mine, but when I put on the Pro Circuits and removed the lid, the stock needles on the middle setting with 260s smoked bad and you couldn't even choke it or it would flood. I had to get the needles and I followed the instructions to the letter and the problem was fixed. Mine needed fatter needles and less taper. The stock needles have a sharp taper to them and the only way I could get mine to idle was put the needle on the first setting and then it leaned way out at half throttle. I live 800 ft above sea level.
My jet settings are now 270 with the lid on needle at middle setting on the Dyno Jet needles and 25 pilots turned to 2 and a half turns out.
With the lid off I run 300s with the needle at the middle setting and 27.5 pilots and turned the air screw 1 and a half turns out.
If you call the tech line at Pro Circuit, Boyesen, Yamaha, and my numerous other sources they all say the Stock needles should work. They never did.