*Get it running at around 30mph and test the front brake only slowly and firmly until its pulling you up...then resume speed and do the same with the back brake only, this will implicate or rule out the brakes.....
*Try accelerating and decellerating on a long wide curve both ways, this will rule out wheel bearings etc...
*Try sudden clutch drops on a smooth surface road to see if the drive is the affected part...
*Park with engine off, hold front brake tightly and have someone pull hard on the front end...this will either clunk or not...if it does not clunk then the headset bearings are fine...if the bike clunks then the headset bearings need checking and/or replacing, at medium speeds this can cause a back end vibration that can seem like the fault is originating at the back...
*Hold down back brake firmly and have someone force the bike backwards jerking it backwards...any clunks are either coming from the caliper or from the swing arm pivot bolts, both can seem very similar...check and correct.....
Alternatively.....Take it to an expert!!!