Another WIN after a long battle.... Just saying if your bike has bad vibes, it should be on the top of the list for the cause. Key note is its present from 4K on up. Mine was always worse at Cruise speed or about 4.8 to 5K. From post: http://www.600riders.com/forum/fz6-mods/54393-vibration-help-2.html
Woo Hooooooooooo!!!!
Finally I've pinned down the vibes! I redid the spark plug caps again and was a bit more aggressive, cutting back the spark plug leads by a good 15mm or more. Also I tried using a wrap of duct tape over the end of the lead, about 1cm wide. Only 2 of the leads were loose (2 and 3), so I just concentrated on them. I also pulled the caps apart and checked the resistance. One had very high resistance so it was cleaned up until the spring made good electrical contact with the brass insert inside the cap. Both caps were in spec so I put it all back together.
I took it out for a spin just after a rain shower, and was amazed! The vibes from 5,000rpm was gone, and it revved cleanly up to 11. I didn't punch it any higher, I was just happy that I don't have to keep looking for the problem. Half way through my ride I got caught in the rain and wind again... my legs were soaked and I was being blown around, but I couldn't wipe the smile off my face! The vibes were much reduced, back to how the bike used to be.
If the vibes come back I can go straight to the spark plug leads and redo them. Not sure how much more I can cut off them, so I've been considering the options of new coils.
The spark plug leads appear to have a plastic clip where they join with the coils, but I haven't seen anyone remove the leads. I hunt around on the net shows that the FZ6R/XJ6 coils have the same primary and secondary resistance as the FZ6, but being a different frame, they could mount in a different position and the leads might be shorter than the FZ6. The photos on ebay ( Yamaha XJ6 XJ6N XJ6F Diversion Ignition Coils Plug Caps LOW Mileage 2009 2012 | eBay ) show a different cap design, but after reading up on the service manual in the electical section it talks about checking the cap resistance, so they must still be a screw on design like ours.
A big thanks to everyone who has helped, especially FinalImpact and TownsendsFJR1300, on this thread and the many other threads on the forum!