You mention looking at the plug caps, I urge you to inspect them before getting more discouraged with the bike. Its less then 1.0 hrs work to fix them all, maybe a little more to measure all the caps.
http://www.600riders.com/forum/fz6-technical/48874-cure-bad-vibrations-spark-plug-caps.html
I caution those who allowed others to work on their bike; Yes, we all want to believe the plug manufactures has gapped the plugs to the spec they said they did however inspection of my NEW NGKs (I used single ground strap CR9E, vrs CR9EK's which have a bigger gap at 0.032") found only one had a gap of 0.028" (manufacture Spec) and all the others were over at 0.03X or more! Because the gap opens as they wear, carbon plugs should be set to 0.027 or less IMO. Exceeding the recommended gap can lead to misfires and vibrations, as will bad connections at the cap to wire junction.
Follow the instructions to the letter and post up your results. Good luck!
EDIT: Define CR9E gap at 0.028" vs CR9EK at 0.032"