[sweetbmxrider]

and it was doing it before you messed with the brakes? when u joints get real bad they vibrate at certain speeds. it can make a squeak/clunk when you accelerate. look at the u joints for grease pushing past the cap seals. maybe get it in the air and have a friend rev it or power brake it and see if the tranny or motor are moving significantly. definitely look over the rear suspension goodies too. peak at the exhaust as well.