I have a 2001 Raptor 660 with some add ons. I got a White Bros E full exhaust syst, K&N Pro design w/outerwears, Dynojet stage two, after market CDI, two 3 inch holes drilled in the box. I had the mains set to the 3000-6000 setting (144L 146R) and it ran terribly at above 6000 ft, now I have the carbs set to Dynojet specs above 6000ft (142L 144R, needle set to the 4th groove from top). I ride mostly above 6000 feet in the dry climate of Utah. Even after the jetting change it still runs the same (same elevation) crapping out at mid throttle while trying to power up a steep incline. After I stop and try to start it back up it blubbers really bad until it eventually revs up and seams to clear out. While on relatively flat trails it seams to run better. It never backfires and revs up to full throttle without sputtering, it's that mid range throttle position under power where it craps out especially when I let off just the littles bit it dumps all power. I hate re-jetting this thing as you know the work it take to just get to the carbs main jets!

The easiest fix is to just get a 06 700R YFI huh?

 

Try running 150/155 jetts in your raptor. Thats what i ran befor i rebilt my motor. Try takeing off your air box lid first to see if that might help it. It sounds like its running to lean.