Mine was an '07 SS donor, I had no trouble with the master cylinder clearing anything. I'm not sure if mine was the same as an '06 or not.
I ran my coolant lines first, on the bottom of the tunnel. I had plenty of space in there, except at the very front where the harness for the BCM came through and got pretty crowded. It wasn't bad though. With a little massaging it fit alright. The wires are flexible.