Get a mechanics stethoscope, online or at a parts store not expensive, listen around the motor make sure it's in the rockers
sounds travel on bikes, and can fool you.
Look for any loose parts, muffler clamps, heat shields, pegs, floorboards, etc.
I had a rattle I couldn't find up front, drove me nuts, found it last night one of the little round covers on the oil tank lines had slipped down and was rattling, I swore it was coming from up front.
