While sitting still and revving up slowly for a few seconds, it hesitates about mid throttle. But when riding there is no hesitation at any time (or I don't notice any). Any thoughts?

stock raptor with snorkle and lid
cut fins with prodesign adapt and foam filter
stock header/pipe with no arrestor
stock jetting
3200 elevation
plug color looks normal (tan)

Other questions: I know the a/f screw needs to be 3 turns out, but what does it effect when its 4 out or 5 out? Does that reduce air or increase air?

Also, how does adjusting the needle clips up 1 or 2 notches affect the carb?

 

If your air screw is on the air box side then the more you turn it out the more air it lets into the pilot circut, thus leaning out the mixture. If it is on the intake side then the more you screw it in the more gas it will let into the pilot circut, thus creating a rich mixture. Usually, from my experience the air screw has been on the airbox side on most Yamahas. You shouldn't run the screw more then three turns out because past that it could vibrate out or come loose. If you find that you need it more then three turns out you should adjust the pilot size.
Your needle is what controls about 1/2-3/4 throttle. At the end of the needle is your main jet, which controls 3/4 - full throttle. There are 5 spots on the needle, the 1st being at the top, and the 5th at the bottom. As you raise the clip you are dropping the needle down inside the bore. Doing this lets less gas escape by. By dropping the clip, you are raising the needle and letting more gas by. As you give it throttle the cable pulls on the needle lifting it out of its bore. Once it is all the way out, at about 3/4 throttle the main jet takes control.

Whenever your checking jetting its never a good idea to rev it in nutural. Doing this is real hard on crank bearings and can cause them to wear quicker then they should. Do proper plug checks at the right speeds to make sure everything is bang on.

 

Don't worry about how it runs sitting still, while it's under a load is what counts.