I just ran into this problem, so I know this won't help the original person who asked the question, but maybe it will help someone else.
I have a 2000 Drifter (800cc). My engine number is on the right side (if sitting on the bike). Aft of the floorboard. Hidden by the exhaust pipe and frame, mounted on the engine and facing straight out toward the frame. It is 13 letters & numbers about 1/4 inch tall. Mine started with VN800AE...followed by six numbers. It took a mirror and flashlight to discover it. My VIN label and engraved frame number where also difficult for me to find, as the former owner had covered the label with black tape so that it would not be an eyesore (white label on black frame) behind the headlight.

