Remove the motor and shaft from the mount.

Put the coupler back onto the shaft.

Drill the 1/4" hole thru the coupler and rod, using the mark you made to make sure the rod is inside the coupler by the proper amount.

The hole should be 3/8" away from the edge of the coupler.

Drill thru both at the same time. You will need some sort of vise to hold it down while you drill.

Double-check that your bolt will fit thru. If not, either re-drill it with a slightly bigger bit, or do another set of holes.