Are you going to Leeds (Robodojo)? if so bring the parts with you, we can have a look then.
Unfortunately not, I had planned to go but then other commitments popped up which I cannot avoid.

Not sure what you are proposing, but need to keep it simple - why grind flat on motor shaft? are you putting bolt through flanged hub shaft and motor shaft then bolting through?
A mistake on my part, I meant on the flange shaft so the nut can seat properly against it. Yes, bolting through.

Is the flanged hub aluminium? If so, you could see if someone would make you one from steel (if you were able to do a basic drawing) then secure it with a couple of decent spot welds to the shaft.
The flange is steel. The side panel where the motor pokes through is indeed unboltable and the hole is bigger than the flange so I could get it welded. Probably the quickest solution.