Need more info on the noise. Try to pinpoint where it is coming from & if at tickover, with clutch in, in gear, blipping throttle, etc....??? Did the service guys give an idea what they thought the noise might be?
Vibrations can cause noises by making handlebar levers rattle or cable rattle against each other or the bodywork. With the latter because the bodywork carries noise around the bike it can seem like engine.
As far as warranty goes unless the bike has obviously been messed about with then if there is a problem the dealer or Kawasaki have to deal with it & fix it to your satisfaction, that's how it is in the UK & I don't think north America is any different.
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Current Kwaks:
'95 GPZ1100S
'03 GPZ500S
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