With 12 discs you should still go alittle higher on the main and dont forget about the needle(move up) to help increase midrange power.

 

Dan, you may just need to raise the needle by installing the clip one notch lower to fix your problem. After that, ride and evaluate. Don't worry about the pilot yet either.....the change may not be necessary.
What kind of filter oil are you using? PJ1 and Maxima Fab1 are excellent choices.

 

I'm using the PJ1 filter oil. I've experimented with the needle in 2 positions so far(3,4) to no avail, it still surges on the top end. What's really weird, the bike used to run a little rich about a month ago, now it seems to be a little lean according to the plug. It also has lost its crisp acceleration and it surges worse on the top end than it ever has before. I've checked the tightness of all the exhaust and intake parts so there doesn't appear to be any vacuum leaks. One thing I've noticed is the surge only happens when I ride on a hard road in 4th and 5th gear at about half to 3/4 throttle. The bottom line is I have not messed with the bike at all in the last month except to ride it, and one day it just seems to lose it's power and run more weird on the top end. Actually, the only thing I have touched is the air filter. I cleaned and reoiled it the day that it seemed to start acting weird. What do you guys think? Thanks for your help!

 

Shot in the dark, but have you tried adjusting your valves? This is a common thing for the valves to be tight and this results in a slow loss of performance when nothing else has changed. Atvtesting.com has a good write up of this. I adjusted mine, they were tight, and I noticed the good ol' power came right back. Mine didn't surge though. I'd also try putting the needle on the recommended 4th groove, adjusting the valves and taking it for a spin.

 

YOU CAN GET PILOT JETS AT YOUR LOCAL YAM SHOP ABOUT 5 BUCKS EACH

22.5 STOCK

25 NEXT STEP UP

 

here is a remote possibility: out here (albuquerque) between nov and march the gasoline is changed to what they call "oxy fuel" this means they add 10% ethanol, which normally only has a small effect (loss of mileage) on most vehicles, but when you take a high performance engine (modded raptor) you can have unusual problems, this same thing (surging and cutting out at high end) happened with a friend whose bike I was trying to jet with a dynojet kit, everything pointed to the needle jet, after trying every combo we could think of I put the stock needle back and it ran fine, out of curiosity I tried some of my racing fuel mix with the dynojet needle and it ran great, the conclusion 10% ethanol will fu$% you up on jetting. just thought I would mention it