Could be an exhaust gasket blowing.
The shift drum would not make any noise, ever. The drum will outlast all of us. All it does is move clockwise and counterclockwise as the rider pushes the shift lever up or down as needed. Go to an empty parking lot or roadway and start out slowly in 1st gear, slowly gaining speed. Does the knock show up? Now go into 2nd gear and slowly gain speed. Is the knock there? Do the same for all the gears. If the knock is only in one or two gears the problem is a broken gear tooth. When the broken gear is replaced, also replace any other gear the broken gear meshes with. Whatever broke the tooth also put the same pressure on the meshing tooth. If the meshing gears are not replaced you will have the pleasure, ( and expense ), of doing the repair all over again when the cracked tooth on a meshing gear decides to break off. This usually happens within the first hour of riding the "fixed" bike. If the test shows no knock in the gears, then chances are the knock is a cam chain needing to be tightened. Please rate my answer. Thanks.
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