A small minority of these bikes do seem to generate more vibration than others: a couple of owners have even sold the bike on as they couldn't fix the problem no matter what they tried. I have a packet of lead fishing weights and FJ1200 bar-ends sitting in the garage ready for installation, but my handlebar vibes are bearable except for very long journeys.
Anyway, possible fixes. As Dudeofrude states, out-of-balance injectors do tend to generate more vibes.
Have you tried riding without any bar-ends attached - vibrations the same or even worse?
Have you checked the engine mount bolt torque settings - unlikely, but might be something there not helping.Pat's invaluable website should make that task easy:
http://www.cartestsoftware.com/fz1/retorquemountbolts.html EDIT: Just re-read & I take it you have a Gen 2 machine? In which case, ignore my link to Pat's FZ1 site. Having said that, you should still check the engine bolts for any anomalies.
Some clarity on your earlier posts, please (maybe I'm the only one who's confused). Did you mean front-end
chatter as in the suspension behavioural characteristic or
shatter as in you suspect front-end of the bike has possibly struck something and there is now unusual vibration coming from the forks?