Hi,
I do know that certain mufflers don't run right when you exchange them between different size engines...
Have you considered:
1: putting a baffle in the end to restrict it more.
2: fitting a a dynojet kit to allow more fuel through (accompanied with a higher flow filter).
If you have a FZR 600 Genesis (4JH), I can supply a brand new exhaust that will run very well on the bike's standard set-up.
It's a bespoke fitment which I have tested myself... Please see pic.
Available in:
Polished stainless
Satin Black (pictured)
Titanium
(also available as a 100mm shorter 'stubby' version)