The drawing calls out for a 4mm counter sink and the alpha parts 3.5mm counter sink.
It is critical that the countersinks on the lower bearing mount side of the motor mount are countersunk to a 4mm diameter. If this is not the case, the M2x6mm FHCS will not sit flush. This causes the motor to not lay flat when mounted and deflects the motor shaft/worm gear into the worm wheel causing binding and the Nema 11 does not spin freely.
This can easily be corrected by using a 4.5mm drill bit with a pointed tip and removing a bit of material in the countersink. I showed @oliver how to correct this on the syringe pump we assembled yesterday afternoon