I just ran into this same problem tonite while installing my six piston Wilwood kit on my 66 Chevelle. The shimming of the bracket wasn't clear at first to me, but after I got a few steps further into the install, found exactly what you found and shimmed it to match up much better. I just don't like how Wilwood doesn't supply safety wire, and new cotter pins with the kit. Now I know why Frank supplies safety wire and pliers with his kits.
This Wilwood thing is fresh to me although we've sold kits in the past, I've been using BAER on my personal cars for 5 years, but on this car thought I'd try something new... I have to say, I'm liking Wilwood so far....