Aye Gary,
OH BOTHER!

Any chance of a photo of this "divot" in the rotor centre? Do you think somebody superglued or centre punched the divot in the rotor and onto the taper to stop the rotor spinning on the taper?

Not sure of the strength of a Yamaha 'original' tool, mine is on loan to Andy230 for use on the race bike and is a three legged puller (casting) for BMC flywheels using 8mm threaded rod and double nuts.
I wouldn't have thought finding the parts overly difficult, but potentially expensive. May I suggest a direct email to Andy230 via 'My messages' on this site from the 'Members List' or contact Slipstream Engineering for a blether?
I would still favour a large HD socket and long bar on the puller when tightening, rather than the impact drill, as you can apply plenty of torque in a controlled way, afore the batter. Seeing that push has come to shove, maybe a 4lb lump hammer or 6lb sledge on a long handle with care might deliver the blow.
I can only wish you well and hope you don't damage yourself, whilst trying to get it to shift.
My regards, Bill.