Had mine dyno'd a few times, although never with the current K&N air filter fitted.
There was always a discrepancy at mid range, but was always told aftermarket exhausts would never match the OEM one on a Fazer, and this fella really knows his stuff.
Rejetting never helped either, tried that and it never ran right at all.
It's a 17yr old bike, don't expect miracles, just enjoy what you've got.