mixture screw), and the position of the clip on the needle, will make the biggest difference regarding the air/fuel ratio, over the broadest range of throttle positions.
As greenpus said, most of the jet kit instructions will leave you richer then needed.
Make sure the bike is warmed up good, before trying to diagnose problems
Look at the Tech Articles page, and read some of the different carb
related articles regarding the PMS, and jetting etc., and that will help.
This is a good read as well.