The area that is slightly milled out is more than likely designed to be the side that the brace installs on, so that the hinge pins can still stick out far enough without there being any slop where the not-milled part installs into the bottom of the bulk ( the milled part sits outside of the bulk, facing towards the centre of the truck ).
The upper arms are designed so that you can install the knuckles in different places ( 2 holes in the end ), which will result in them either having zero or several degrees of caster. I would install the front & rear uppers so that the holes are towards the rear, allowing you to have greater caster angle on the front knuckles, and zero caster angle on the rear knuckles.
The metal parts that came with the towers are spacers/ stand-offs for mounting your shocks- you can see them in the picture you linked to and they work like any other shock spacer ( you need one long screw to go through both shock caps & spacers ).
The lack of instructions is seen as an IQ test- if you can figure it out for yourself then you passed; if you couldn't however...