Totally baffled by your statement that eco mode causes vibrations. Makes no sense that it could happen, and I've never heard anyone else complain about it. I have 28,000 miles on mine and I run it 95% in Eco mode, as does the guy I ride with every weekend. Running leaner would not have any way of making a bike vibrate more.
I never thought it should matter either, but it does on my bike (which came from the factory with rediculous amounts of vibrations).
I rode almost exclusively in ECO mode for the first year, then discovered the huge hesitation when cracking the throttle on steep downhills in low gear was MUCH worse in ECO mode. I started using non-ECO mode, and as a side effect, noticed less vibrations in the bike. After that, I played with it for awhile, and there is definitely more vibrations when it's in ECO mode.
For some time now, I've suspected my excessive vibrations were related to fuel mixture, fuel timing, or flow through the motor. When I installed the K&N air filter, the vibrations were reduced quite a bit. Adding the cat free ZX-14 exhaust with the fully open Two-Bros slipons also reduce the vibrations a little more, although I lost that gain when I took steps to reduce the noise (probably added back pressure).
Sometime this winter, when I find some spare time, I'll run through the valves and sync the throttle bodies. I'm hoping that cures the vibs, because if it doesn't, I'll probably be parting with the bike.