Hey Juice you should cut a window in your case, show off the redness!
The Zalman's aren't too friendly, I've cut myself numerous times when I was still using mine.
Moving up the HDD's would help with GPU temps, since there is more direct airflow going to them.
I don't even try front audio jacks. There really needs to be a standard plug for that.
You could try moving your CD drive down a spot and sticking wires in there, or behind the drive mounts. Also, if you can flip the hard drives around, you can hide the plugs better.