If you cut nearly the whole top off your airbox, you didn't do the 3x3. You did whatever size opening you have. Your jetting is off, because all of the information available revolves around stock airboxes, and ones w/ a 3" by 3" opening. You're going to have to tune it on your own w/ a larger opening. It makes a big difference in the jetting specs., that's why all the information says to cut it exactly 3" by 3". A stock engine has no use for any more airflow than is privided by said "3x3 mod" anyways. Tape off a 3" by 3" opening and ride it to see how it responds. Did you do the pilot circuit test to determine if you need a larger pilot jet? Bigger doesn't mean better, and the pilot circuit has nothing to do w/ the running performance of the bike.