The spacers go into the holes on the caliper, and the flanged part goes between the caliper and the fork leg. The wave washers go under the bolt head. As far as your splitter, my '81 has dual discs, but is mounted differently than an LS, so I can't help you out there.
Bob, what you are describing sounds a little like the "top hat" used on the wheel bearing assembly. Different size, of course.
Bob Grauer replied on Boxerworks:
"Rob, when I installed a set of these [rotors] on my '93 R100RT some time ago I had a similar problem. What I found was that I needed to shim the caliper (2 piston Brembo) so that the rotor was perfectly centered. Thereafter the rotor made minimal noise."
?
But if you put the "top hat" spacers
inside the hole on the caliper, that would probably make the hole too small for the stock screw to fit.
I guess I will find some thin shim stock and make my own.