I have a 2001 Raptor. I have had to replace like every freaking thing, but i need to get the jetting right. I have a Full Yoshi pipe kit and a K&N Filter and cant get the jetting right. It loads up on bottom end but if you keep your thumb in the throttle, it runs like a dream.

 

ummmmmmmm, try the yamaha message board?

 

If it runs like a dream at full throttle you answered your own question. (keep it full throttle[img]i/expressions/face-icon-small-wink.gif[/img] )
Ok it sounds like its rich, when running full throttle you are letting more air in to lean the mix, and loading on the bottom usually means to much gas. But as far as jet sizes you really would be better off in the Yamaha forum, they would be able to relate a little better.