what a bummer, I would actually like a nice exhaust. with dirt bikes they make a significant improvement. I have a real hard time spending that kind of coin just for looks.
I couldn't justify the expense, either.
Going to a less restrictive exhaust has the potential to allow more of the motor's work to spin the back wheel.... but that only works if you can get at the point where the restriction is greatest, and reduce it there.
With the FZ6, the intake is fairly corked up to reduce intake 'honk', the catalytic converter is relatively restrictive, and the automotive muffler under the seat is quite heavy.
Losing the cat, and going to a lighter muffler/muffler set as well as opening up the intake to allow more airflow will make the bike slightly lighter (maybe 5-10 lbs), louder, and has the potential to make it run worse than OEM.
Once you have it breathing with less restriction, you now have to make sure the fuel air mixture is correct. You may have to invest in a 'map able' ECU to get a measurable gain in HP.
When it's all said and done, a pipe system from the header back + an ECU, plus dyno time, you may gain 5-8 HP. This will be at the expense of reduced MPG, as well.
Buying all those parts brand new, it works out to well past $1,000. Add in labor, if this is beyond your comfort level....
As I have replaced the FZ6 with a Kawasaki ZX6 which has a K&N air filter and a M4 exhaust --- I can say the FZ6 is close enough in performance that I wouldn't change it from OEM if I had to do it again.
Having to wear ear plugs to ride the Ninja, and having the motor sputter and pop constantly in low RPM situations makes the bike less enjoyable than it might be. I do like the sound of it --- but I can wholeheartedly agree that I get far more attention from the LEOs than I would with an OEM exhaust.