skid,
I have 4 allen bolts (M5 x 20), and everything you have, including no drawing or instructions. You are missing a bolt. My take on the threaded rod is its an installation tool for the front bracket. You thread it into the bracket, place the bracket on the frame, and pass the rod through the hole in the plate as you position it. Now you can pull the bracket down with the rod and install the other bolt. Rear brackets just seem like they would loosely stay with the plate. The studs on the pipe clamps must replace a rubber insulator in the pipe guard, and the stack of fiber washers is to adjust fit on the pipe. The red rubber washers appear to be high temp silicone with an M5 hole, and probably go on the clamp studs last, so they contact the pipe guard and function as insulators.
Of course, I don't have a bike here yet to verify this, but its my best guess. Next week I'll know.