I just want to make sure that you're aware that those rear brackets are slightly 'tweaked' from the factory, but if you are lining them up with the running board brackets, you should be fine.
I had quite a time aligning all of my metal on the truck in general. I started with the body 'loose' and aligned the front clip. Then, I hung my rear fenders and running boards and moved the entire body accordingly to ensure proper side to side gap on rear fenders, then I tighten body and split the difference in gaps with the front end and tightened. Then, I adjusted rear fenders, tightened, and played with the running boards and fenders for quite some time. I have a 1/4 in gap between fenders and rear of running board, and I'm going to live with that. I haven't bolted the fenders to the running board because I'd stress the metal more than I would want. I'm not sure if that was the right way, but most of the other panels line up just fine.
