40 seems a very small pilot most run a 45 and I wouldn't go less than a 42 with your set up, but that all depends on where you live. Never just set your mixture screws, you need to adjust them the right way. That is also a good way to tell if you have the right size pilot jet in there. Then you have to consider that your pilot size will effect your main size and then the needle will play into that as well. You need to find someone that lives at a similar altitude that has done the work to set up their bike the right way, then you could use that as a starting point or Pats calculator will also give you a good starting point. Once you think you are close the only way to do it right is a Dyno run then adjust...repeat until jetted right.

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