I run 87 octane in my GenII at the track because it makes more power. Besides being more likely to detonate, lower octane fuels typically burn faster and sometimes have more BTUs (depending on the fuel) In fact MR9 and MR11 are both low octane race fuels designed specifically for bikes like the GenII Hayabusa. Detonation has a lot to do with head / piston design, and cooling, and the GenII does very well even with all that compression.
Your autoshift needed more delay because you are pulling harder at redline with the lower octane fuel.
Remember, if you did everything your owners manual told you to do, you would never go over 65 mph, or wheelie, or do burnouts, or ...