Are you running a power commander with mapping for the aftermarket cans? If so, did the map richen the mixture at all? If so, the stock cans may restrict the flow causing an overly rich situation. That's all I got.
BTW, my '99 sometimes has a smell of gas. I usually get in the low 30 mpg range of mixed riding. I do have a tough time of keeping my wrist from twisting too quickly though.