I had the same bike and the same thing happen to me... It's the Woodruff key on the flywheel. It has sheared off and now your timing is off.  It's a cheap part and pretty easy to fix. The biggest problem was getting a flywheel holder to hold the flywheel to tighten everything back up.

thnx for the reply man, i will tear it down tomorrow and have a look... i was wondering, cause it doesnt matter where i set the timing, it still backfires

k i have a previous thread stating everything i have tried with this bike... so i went back out today to make sure i didnt F the timing up... one of the depression marks is hidden behind the little clip on the cam sprocket, so i removed it, and sure enough i appeared to be 180 out, so i flipped the sprocket 180 lined the 3 depression marks up 2 with the head and one at 12 o clock, 2 on the cam are up and the I is lined up in the window. Threw it all back together and now i get some valve noise? im assuming, and still can not rev my bike. i need help!! Im not overly mechanically inclined, but im not ovlivious either, everything i have tried i learned off youtube google and the forums.

cmon there has to be a rappy somewhere with this same issue!!

I bought a 2001 raptor 660r 2 days ago, took it out on a short test drive and the bike ran perfect. Got the bike home, unloaded it and took off for my first ride. Made it about 20min down the road and this is when i started to have problems.
I was in 4th gear WOT, shifted into 5th and got sputtering, spitting, and backfiring. I had to crawl home under 1/8th throttle any more and it would quit, so this is where i am at now.
I first called the seller to see whats up, they said the only problem they had was transmission(of course its an 01, was replaced with an 03 tranny) ad a sticky choke cable. The bike sat for a while so i changed the gas, new spark plug, took the carbs off and thoroughy cleaned them, put it all back together and same thing. I took the reverse limiter? (down by the front sprocket) grounded that to the battery. Still same thing. I seen online everybody has a problem with their parking brake rev limiter malfunctioning so i cut the wires right off(still connected at the handlebars) and now the black and the green wires are free. If i splice those together, i can not rev the bike at all, will only idle, if i seperate the wires, i can rev the bike but it spits and backfires. So i checked my timing, cam at TDC, line up perfect with the 3 dots on the cam sprocket, and the I in the window. I am out of ideas. Somebody please help me.