First things first. Engines are usually creamy smooth, well mine is. So as been said something could be loose.
Check all engine mounts bolts.
Vibes can also come from carbs out of ballance. Worth a look.
Now suspension?
Front::Its very undersprung in the front, so fit some .90 springs.
The dampers are way to harsh on low speed damping & too soft on high speed damping. You will need to get your forks re-valved. That with the new springs should be a huge improvment.
Rear:: Spring are fine, but again the dampers are the issue.
You will need to get them serviced, & a re-valve. That should fix the backend.
Other than that, it Ohlins all round & your wallet will hate you, not to mention the wife will kill you.$$$$$$$$$$$$
Here's a very interesting read. I have my 05 ZRX forks & shocks there now being done. I execpt them back in the next few days, so I'll give my thoughts on their work then.
http://www.promecha.com.au/project_zed.htm