Mine had a similar problem until i replaced the battery.
I told it before here i think. the battery was strong for cranking, but could not provide the voltage (or current) for the 961 ignition and/or injection any more. That same battery did fine from then on in my Thruxton for about a year, and now in my old commando.
Not saying it is this, but worth checking. Mine felt like another bike after replacing it.