Unless there is a significant difference in the design of the big bore and its predecessors there could be as many as three ways of altering the alignment. The Myford motor mount is slotted so you may be able to shift it along them. The motor base may also be slotted giving more flexibility. Finally you may be able to more the pulley along the shaft of the motor.

It may not be the motor out of alignment but the other end of the operation, the countershaft. The pivoting arms that support the countershaft and allow for belt tension adjustment are a bit flimsy on the Myford and prone to bending out of shape over the years due to incorrect adjustment and wear. So make sure if you can that the countershaft is sitting properly in line with the headstock spindle before you align the motor to the countershaft. Make sure the two belt tension adjusting screws are protruding an equal amount and both are touching on the cam surface. Also check that your pulleys are running true as this can give a false alignment reading if one pulley is a bit wobbly and you apply the straight edge to it.

That said, it's a rubber belt so 1mm of misalignment will not cause the end of the world. Doubtless the perfectionists will disagree.

Perhaps I'm stating the obvious but is there is pulley misalignment yet the shafts are parallel the simple act of laying a straight-edge across the pulleys will produce a "wedge" of light. Is that what is happening?