Hey fellows I am doing this on my truck now and was curious if you found a solution
Best advice that I can offer is to lay the running boards on the brackets without any bolts attached to the running boards to see if your brackets line up with the holes on the underside of the running boards, and to see if the holes in the end of the running board lines up with the holes in the rear fender. If they do, go get a bunch of one dollar bills and start handing one to as many perfect strangers that you can find.

Next, install the special running board bolts to the underside of the running boards install the running board, and install the nuts. Don't tighten them up yet.
Install the bolts that hold the running board to the rear fender. There is a piece of felt that goes in between. don't tighten those yet either.
Install the apron, and apron bracket to the running board. Don't tighten those up yet either.
Now you can start tightening bolts.
I start with the bolts which hold the end of the running board to the rear fender.
I then tighten the apron nuts and bolts.
I then tighten the running board to brackets nuts.
If I have installed new running board brackets, I tighten those bolts to the frame last.