Here is my procedure for making handle nuts.
First, file the top of your appropriately sized rod.
Then, cut the slot with a hacksaw. Test the depth with a screwdriver.
On the other side, drill the hole for the threaded rod using the correctly sized drill for the tap, this is where the threaded rod goes.
Then tap, making sure to use a cutting fluid. Use tape to show you when to stop. You cannot tap where you have not drilled.
Finally finish with sand paper. It works very well to mount the steel low down in the vice and bring the paper to it, than try to bring the piece to the paper.