Am running the exhaust back from the headers and am thinking the e-brake cables will be sitting on the pipes, does that sound right, or am I running the pipes not low enough? I really want to keep the pipes as close to the bottom of the car as possible, if possible.
That is correct. I have had several different exhaust setups and many have had the cables resting on the top of the pipes. Never seemed to interfere with anything. Just left scratches on the pipes after a while.