This all sounds very interesting. And very timely.
I have taken my 07 1200GS to 2 shops already to try to fix the 'lumpiness', most noticeable when the enging is warm and in the lower end of the rpm range and at idle. Feels as if the motor is being strangled somehow.
To date they have tried 3 solutions:
swapping out the oxygen sensors for known good ones - didn't work;
cleaning the 'gum' out of the throttle bodies - no difference;
installing a new version of the ECU 'firmware' - some improvement but still not as smooth and free running as I'd like.
My next step was going to be to buy a PC. My local dyno guy says he can do a map for each cylinder, which sounds like what is needed if the hex head motor is, in fact, fuelled and sparked like 2 engines.
Poolside, you mention that the CAN BUS version of your 'solutions' are further down the track. Like how far?
More power to you and keep up the good work.