tin on a tdi (trying to rember what one though??) has captured nut... id try to fab that nut into it... has a cage to keep it in place...
That pulley lined up perfectly before and needed absolutely NO material removed in order to fit a 13mm socket on those nuts. Done it about 75,000 times personally haha.
For balance, you could make the three holes that are in front of the three pump fasteners match and then make the other three holes match. Make a bushing for your alignment pin. Mark the correct hole because you'd then have two 'stupid' holes.