I really cant remember what I did with the wire hanger on the bottom. I'm gonna guess and say I removed it. Does that have something to do with the rear exhaust hanger?...I never had those on my bike, so things went together differently under there for me.
Crank case breather I have mounted to that little black tab next to the sprocket cover which holds the wires back next to the engine. I drilled a hole in the tab, and mounted it upwards on the sprocket cover, then bolted the filter to it. I thought I had a pic in this thread somewhere towards the begining.