Hello,
I'm not positive on the 250's, but I know that the 98+ 400's are jetted way leaner than the 96/97 models. They are good stock, but any airbox/pipe mods will increase airflow, thus leaning out the mixture. Maybe he could just adjust the airscrew to compensate, but rejetting is probably needed to fine tune the mixture. Put in a new plug, and pull it back out after a short time of riding. It should be a darker charcoal, or brownish color. Black and sooty means to rich, light grey or white means to lean. Good luck.