OK, I think I've got it now. You're trying to locate the channel type mounting brackets that go on the running board itself.
You're right about most of the drawings in the FAM being '54. I flipped thru my copy and saw only a few with a '53 date on them.
I agree that the critical thing is to get the joint at the rear fenders correct, but I'd think you just need to get within 1/8" overall. The reason I say that is the rear fenders are bolted to the bed, which is bolted to the frame and there's definitely some fore-aft slop available at both places.
I may be out at my truck this weekend, which still has the running boards mounted on it, and get some measurements for you. But even then that may not get you what you need as the mounts on the bottom have rusted away or collapsed over the years. The front driver's side has bolt heads sticking thru the running board and the right front fender has taken a pretty good hit. But if those measurements will help you, I'm happy to do it for you.
You may be right about the best approach being waiting till you get at least the bed and rear fenders in place to locate the brackets on the running boards.
Kevin