I think the running boards need to be removed so that the tabs along the bottom edge of the door sill can be released. Then remove the screws in the face of the sill and lift up to release it from the rolled strip of metal that is welded to the floor.
The running boards haven’t been on my car for many years, so I can’t remember how large the gap is between the boards and the door sill. I am glad to hear you already had a replacement pair on hand.