Could it be that the 01 computer although 16 bit, is pinned out like the 02-07's? Kind of like a transition year to support the new harness to be used on the 01-07 bikes. I see that 99-00 used a different computer than the 01 and the 02-07.
Update 31 MAR - I have ran the bike a few times and there does not seem to be any issues. I have not swapped the crank pickup wires underneath the tank and the times it has been under wide open throttle (up to 10K rpm) there has been no hesitation so I will monitor.