I like the idea of placing the steering shaft through the header to get it to be equal length. As it looks right now, it is sitting to close to the coupler. With engine movement and an engine mount going bad (pasn side rubber gm part), I would like a little more room for error. I do realize in installing it the way suggested may cause one small issue. When removing the trans, the headers will have to be removed - meaning the driver side header may need to be taken out completely which may mean you need to undo the steering shaft...something to think about. Or we might be able to unbolt the header and slide it around to remove the trans.
As for the flange location, I was running a 3'' inch SS exhaust on my car that was very well made and tucked under the car. I still managed to scrap the exhaust on speed bumps, pulling into slightly steep driveways and such. Something else to keep in mind. We don't want to be tearing up brand new SS headers