It would be interesting to see a pic of the underside of the doors. I've checked every info source I have and I can't find any 41 GM vehicles with running boards (other than trucks). They aren't 40 doors as the quarter window line is straight on the 40 and the 41 is slightly curved as yours is. I'm wondering if someone didn't shorten the doors when the body was installed on that chassis. If so then the easiest option would be to just make some custom running boards and then let everyone wonder what's different about it.
"Instructions are just the manufacturers opinion of how it should be put together". - Tim Allen