I was just curious as to your starting point, if you were subtracting fuel from the stock map with a rich AFR that would have been a bit strange, but from an existing map makes more sense.
I've had the head shake while accelerating as I believe its a result of the suspension becoming unloaded due to the torque but never while slowing down or braking. The only things I can think of are the condition of the front tire, poor road condition, really high pre-load on the forks, or REALLY bad steering geometry (ie, if you raised the rear of the bike by a large amount and lowered the front significantly). Since you thought it might have something to do with the suspension bouncing you could try adjusting the rebound or compression dampening to see if it helps, 1 or 2 clicks makes a pretty big difference, so write down and check each of your changes. There's others of this forum that would have better advice on this though.
The .1 difference between the target AFR and the measured AFR could simply be slight differences between the cylinders (ie 1 & 4 vs 2 & 3), for example if the outside cylinders are running slightly lean and the inside slightly rich the difference between exhaust pulses would create a minor variance. There could also be slight changes in the road condition that would be affecting the load on the engine which could change the fuel requirements slightly or a whole host of other scenarios.
Sounds like you've got your map adjusted pretty well at this point, I hope you get some time before the end of the season to go out an just enjoy the ride!