I've looked over my Yamaha sales brochures from 1998 and 2001.
Looks like your bike does have a matching frame, seat, and fuel tank as far as I can tell.
I wonder about the mounting bracketry that attaches fuel tank to frame and whether or not the airbox, itself, is for a 1999 model.
Are there any markings like 4XV or 5JJ molded into the airbox inside or out?
Is the air filter element inside oval-shaped or flat?
Does the air inlet sit on top of the airbox and face rearward or does the air inlet come from the lower front (although I kinda' doubt this is the problem, but, who knows?).