Glen,
It could be many things including and not limited to; gearing, cams, compression, condition, valves, springs, cam followers, porting, dragging brakes, flywheel/piston weight...
I recall a few years ago I was racing a norton 750 atlas (before I saw the light) with a fellow competitor who had the same model bike (his had a commando engine) and from what he told me in a higher state of tune: It always used to wind him up that my motor could routinely out accelerate him , so he just couldnt beat me. Arguably they were both comparable both being norton twins but they weren't the same. I guess if I had owned the slower bike I would have looked further so I understand you'd like your super rocket to be on the par you would expect.
Tim