Im not really following where you think the issue lies?
See, I think the OP is talking about the actual holes drilled into the rotor itself. On the OEM one the holes are offset to each other so none actually line up wrt a line from the axle outwards. While the ness ones have the holes drilled in line to the axle, such that you end up with 2 hole lined up all the time.
No idea if its the cause or not, but the hole pattern on the Ness certainly leaves bugger all disk surface in play when compared to the factory setup.
John i can see there is no "disc centre" the buttons are not of the type i know you mean. They are in fact the bolts that fix the disc to the hub and only contact the disc in half a hole!
The holes look square and sharp edged in the pics, no shamfer or counter sink at all
Isnt that how those discs are fastened stock though? Same as VROD etc, the stock discs look the same.
So does the pulse correlate with the holes? Not the best at the maths, but looking at your rotor, you've got 6 double drilled holes per segment, 5 segments so 30 pulses per wheel spin.
Due to the design checking for runout with a dial gauge will be difficult, buy that would be my next move, you could try a straight edge but qould need to remove the wheel. Maybe the disc isnt sitting 100 % flat on the hub.