u mean the weld that u just had done, is touching it? was this weld to repair damage caused from the engine vibrating against the swinger to begin with?
the motor does sit close at the back, but ill bet the problem is a slightly obrounded swingarm bolt hole. measure it with calipers it might not be too noticeable by the eye.
if you are only an index card thickness away from your swingarm as it sits, you only need a index cards thickness of slop in the hole for it to smack it.