Smart,
In my experience you don't modify the output shaft, you modify the drive cone. There may be exceptions to this, I just have not run across them.
You have to drill a hole in the drive cone to allow it to slip over the output shaft. You then drill and tap a hole in the side of the cone for a set screw to lock it to the output shaft. The set screw can lock well by screwing into the flat on the output shaft if it has one. Works the same whether it is an automotive or motorcycle starter.
Your motto says "CA can fix anything!". Maybe you can just try CAing it on.
Ken