So assuming the holes all line up and are across the ctr of the rod and you have a mill.
Clock the vice in to ensure it is true along the X axis. Clamp the bar in the vice supported on parallels with a little sticking out one end.
Use an edge finder to locate the end and move half the finders diameter and zero the handwheel or DRO, then use it to either touch one side of the rod then zero dials and move over half x (rod plus edge finder dia) or if you have a DRO touch one side zero Y, touch the other side and use the 1/2 function to get th emid point. If no edge finder then use the shank of the spot or ctr drill to touch off.
With the spindle now directly over the middle of the rod and one end put a spot or centre drill into the chuck and move along Y to the position of the first hole and spot, change to the 1.5 drill and complete the hole not forgetting to remove the parallel before hand. Move along to the next position and repeat, ditto the third.
All holes should be positioned to 0.001″ or 0.005mm
If that does not make sense, then just say so and I’ll go and drill a bit of bar tomorrow and record it.
Or take a look at my current Kelsey thread, the two parts covered so far use the same methods to place a number of holes and it makes no real difference if it is into a flat stock or a round bar.